hg19 LOSS chr16-28786642-29061036

Length (hg19) : 274,394 bases - Length (hg38) : 274,394 bases

CNV-Hub AChro-Puce
PIEV

Variation found in the list of recurrent CNVs known to be predisposing factors for neurodevelopmental disorders (NDD) established by the French working group AChro-Puce.
PIEV (16p11.2 distale)

De novo or inherited from symptomatic parent

Inherited from asymptomatic parent

Unknown

AChro-Puce Criteria taken into account¹

Class

2 Major

CNV inherited from Asymptomatic parent

Class

4 Major

De novo CNV or inherited from Symptomatic parent

Class

4 Major

At least one occurrence in patients databases as pathogenic or likely pathogenic

Class

4 Major

Haploinsufficient gene

Class

4 Minor

CNV more frequent in Coe & Al patient cases than in controls

Class

4 Minor

At least one occurrence in patients databases as pathogenic or likely pathogenic > 50 % overlaps

Class

4 Minor

No occurrence in DGV / DGV-Gold > 50 % overlaps

ISV²

XCNV³

ClassifyCNV ACMG⁴

AnnotSV ACMG⁵

ACMG criteria

ClassifyCNV

2A
+ 1

Complete overlap of an established HI gene/genomic region.

5B
-0.45

Patient with specific, well-defined phenotype and no family history. CNV is inherited from an apparently unaffected parent.

5D
+ 0.45

CNV segregates with a consistent phenotype observed in the patient’s family.

AnnotSV

2A
+ 1

Complete overlap of an established HI gene/genomic region.

5B
-0.45

Patient with specific, well-defined phenotype and no family history. CNV is inherited from an apparently unaffected parent.

5D
+ 0.45

CNV segregates with a consistent phenotype observed in the patient’s family.

Diseases :

Gene	Disease	Source	Inheritance
SH2B1	Severe early-onset obesity-insulin resistance syndrome due to SH2B1 deficiency	Orphanet	Autosomal dominant
ATP2A1	Brody myopathy	Orphanet	Autosomal dominant, Autosomal recessive
CD19	Common variable immunodeficiency	Orphanet	Autosomal dominant, Autosomal recessive, Not applicable
TUFM	Combined oxidative phosphorylation defect type 4	Orphanet	Autosomal recessive
LAT	Severe combined immunodeficiency due to LAT deficiency	Orphanet

ClinGen

0 benign CNV
0 likely benign CNV
0 uncertain CNV
2 likely pathogenic CNV
31 pathogenic CNV

70% Overlaps

Decipher

0 benign CNV
43 unknown CNV
10 uncertain CNV
33 pathogenic CNV

70% Overlaps

DGV-Gold

0

80% Overlaps

0

50% Overlaps

DGV

0

80% Overlaps

0

50% Overlaps

Coe & Al study⁶

5

Patient cases
70% Overlaps

1

Controls
70% Overlaps

Genes with pHaplo > 0.55⁷

2

ATXN2L

Genes with pTriplo > 0.68⁷

4

ATXN2L TUFM SH2B1 SPNS1

Genes in SFARI

0 Genes in OMIM

9 Sources and references

1 : AChroPuce Consortium Recommandations pour l’interpretation Clinique des CNV (Copy Number Variations) Septembre 2022.

2 : Automated prediction of the clinical impact of structural copy number variations : M. Gažiová, T. Sládeček, O. Pös, M. Števko, W. Krampl, Z. Pös, R. Hekel, M. Hlavačka, M. Kucharík, J. Radvánszky, J. Budiš & T. Szemes View article

3 : Zhang L, Shi J, Ouyang J, Zhang R, Tao Y, Yuan D, et al X CNV genome wide prediction of the pathogenicity of copy number variations Genome Med 2021 13 132.

4 : Gurbich, T.A., Ilinsky, V.V. ClassifyCNV: a tool for clinical annotation of copy-number variants. Sci Rep 10, 20375 (2020). View article

5 : Geoffroy V, Herenger Y, Kress A, et al. AnnotSV: an integrated tool for structural variations annotation. Bioinforma Oxf Engl. 2018;34(20):3572-3574. doi:10.1093/bioinformatics/bty304

6 : Coe BP, Witherspoon K, Rosenfeld JA, van Bon BWM, Vulto van Silfhout AT, Bosco P, et al Refining analyses of copy number variation identifies specific genes associated with developmental delay Nat Genet 2014 46 1063 71

7 : Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, et al A cross disorder dosage sensitivity map of the human genome Cell 2022 185 3041 3055 e 25

Delete and Recompute CNV

9 OMIM Gene overlap(s)

Download genes as .csv

RABEP2 NM_024816.3 Whole gene - Size : 32,105 bases

pLI : 0 LOEUF : 0.57 sHet : 0.015 pHaplo : 0.3 pTriplo : 0.53
Location : 28,915,742 - 28,947,847

Database :

DecipherGenomics OMIM:611869 GTEx Portal Human Protein Atlas Ensembl

SH2B1 NM_001387430.1 Whole gene - Size : 27,612 bases

pLI : 1 LOEUF : 0.23 sHet : 0.101 pHaplo : 0.5 pTriplo : 0.96
Location : 28,857,921 - 28,885,533

Disease : Severe early-onset obesity-insulin resistance syndrome due to SH2B1 deficiency

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:608937 Orphanet:329249 HGNC:30417 PMID:23160192 GTEx Portal Human Protein Atlas Ensembl

Human Phenotype Ontology Show/Hide

HP:0011968	Feeding difficulties	Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it.
HP:0002020	Gastroesophageal reflux	A condition in which the stomach contents leak backwards from the stomach into the esophagus through the lower esophageal sphincter.
HP:0000717	Autism	Autism is a neurodevelopmental disorder characterized by impaired social interaction and communication, and by restricted and repetitive behavior. Autism begins in childhood. It is marked by the presence of markedly abnormal or impaired development in social interaction and communication and a markedly restricted repertoire of activity and interest. Manifestations of the disorder vary greatly depending on the developmental level and chronological age of the individual (DSM-IV).
HP:0000294	Low anterior hairline	Distance between the hairline (trichion) and the glabella (the most prominent point on the frontal bone above the root of the nose), in the midline, more than two SD below the mean. Alternatively, an apparently decreased distance between the hairline and the glabella.
HP:0001250	Seizure	A seizure is an intermittent abnormality of nervous system physiology characterised by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain.
HP:0000733	Abnormal repetitive mannerisms	Use of the same abnormal action in response to certain triggers or at random. They may be used as a way to regulate one's internal state but must otherwise have no apparent functional purpose.
HP:0000175	Cleft palate	Cleft palate is a developmental defect of the palate resulting from a failure of fusion of the palatine processes and manifesting as a separation of the roof of the mouth (soft and hard palate).
HP:0003077	Hyperlipidemia	An elevated lipid concentration in the blood.
HP:0000735	Impaired social interactions	Difficulty interacting with others through emotional, physical, or verbal communication.
HP:0001646	Abnormal aortic valve morphology	Any abnormality of the aortic valve.
HP:0002910	Elevated hepatic transaminase	Elevations of the levels of SGOT and SGPT in the serum. SGOT (serum glutamic oxaloacetic transaminase) and SGPT (serum glutamic pyruvic transaminase) are transaminases primarily found in the liver and heart and are released into the bloodstream as the result of liver or heart damage. SGOT and SGPT are used clinically mainly as markers of liver damage.
HP:0001161	Hand polydactyly	A kind of polydactyly characterized by the presence of a supernumerary finger or fingers.
HP:0011800	Midface retrusion	Posterior positions and/or vertical shortening of the infraorbital and perialar regions, or increased concavity of the face and/or reduced nasolabial angle.
HP:0002119	Ventriculomegaly	An increase in size of the ventricular system of the brain.
HP:0000708	Atypical behavior	Atypical behavior is an abnormality in a person's actions, which can be controlled or modulated by the will of the individual. While abnormal behaviors can be difficult to control, they are distinct from other abnormal actions that cannot be affected by the individual's will.
HP:0000556	Retinal dystrophy	Retinal dystrophy is an abnormality of the retina associated with a hereditary process. Retinal dystrophies are defined by their predominantly monogenic inheritance and they are frequently associated with loss or dysfunction of photoreceptor cells as a primary or secondary event.
HP:0000347	Micrognathia	Developmental hypoplasia of the mandible.
HP:0000337	Broad forehead	Width of the forehead or distance between the frontotemporales is more than two standard deviations above the mean (objective); or apparently increased distance between the two sides of the forehead.
HP:0008763	No social interaction	Lack of intentional participation in interactions with another person.
HP:0000076	Vesicoureteral reflux	Abnormal (retrograde) movement of urine from the bladder into ureters or kidneys related to inadequacy of the valvular mechanism at the ureterovesicular junction or other causes.
HP:0000256	Macrocephaly	Occipitofrontal (head) circumference greater than 97th centile compared to appropriate, age matched, sex-matched normal standards. Alternatively, a apparently increased size of the cranium.
HP:0002691	Platybasia	A developmental malformation of the occipital bone and upper end of the cervical spine, in which the latter appears to have pushed the floor of the occipital bone upward such that there is an abnormal flattening of the skull base.
HP:0000729	Autistic behavior	Persistent deficits in social interaction and communication and interaction as well as a markedly restricted repertoire of activity and interest as well as repetitive patterns of behavior.
HP:0001266	Choreoathetosis	Involuntary movements characterized by both athetosis (inability to sustain muscles in a fixed position) and chorea (widespread jerky arrhythmic movements).
HP:0001508	Failure to thrive	Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm.
HP:0001319	Neonatal hypotonia	Muscular hypotonia (abnormally low muscle tone) manifesting in the neonatal period.
HP:0007166	Paroxysmal dyskinesia	Episodic bouts of involuntary movements with dystonic, choreic, ballistic movements, or a combination thereof. There is no loss of consciousness during the attacks.
HP:0002808	Kyphosis	Exaggerated anterior convexity of the thoracic vertebral column.
HP:0006863	Severe expressive language delay	A severe delay in the acquisition of the ability to use language to communicate needs, wishes, or thoughts.
HP:0004322	Short stature	A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms).
HP:0000003	Multicystic kidney dysplasia	Multicystic dysplasia of the kidney is characterized by multiple cysts of varying size in the kidney and the absence of a normal pelvicaliceal system. The condition is associated with ureteral or ureteropelvic atresia, and the affected kidney is nonfunctional.
HP:0002251	Aganglionic megacolon	An abnormality resulting from a lack of intestinal ganglion cells (i.e., an aganglionic section of bowel) that results in bowel obstruction with enlargement of the colon.
HP:0002149	Hyperuricemia	An abnormally high level of uric acid in the blood.
HP:0002650	Scoliosis	The presence of an abnormal lateral curvature of the spine.
HP:0001249	Intellectual disability	Intellectual disability, previously referred to as mental retardation, is characterized by subnormal intellectual functioning that occurs during the developmental period. It is defined by an IQ score below 70.
HP:0000405	Conductive hearing impairment	An abnormality of vibrational conductance of sound to the inner ear leading to impairment of sensory perception of sound.
HP:0000902	Rib fusion	Complete or partial merging of adjacent ribs.
HP:0000776	Congenital diaphragmatic hernia	The presence of a hernia of the diaphragm present at birth.
HP:0009088	Speech articulation difficulties	Impairment in the physical production of speech sounds.
HP:0410263	Brain imaging abnormality	An anomaly of metabolism or structure of the brain identified by imaging.
HP:0001513	Obesity	Accumulation of substantial excess body fat.
HP:0002280	Enlarged cisterna magna	Increase in size of the cisterna magna, one of three principal openings in the subarachnoid space between the arachnoid and pia mater, located between the cerebellum and the dorsal surface of the medulla oblongata.
HP:0007099	Chiari type I malformation	Arnold-Chiari type I malformation refers to a relatively mild degree of herniation of the posteroinferior region of the cerebellum (the cerebellar tonsils) into the cervical canal with little or no displacement of the fourth ventricle. It is characterized by one or both pointed (not rounded) cerebellar tonsils that project 5 mm below the foramen magnum, measured by a line drawn from the basion to the opisthion (McRae Line)
HP:0001328	Specific learning disability	Impairment of certain skills such as reading or writing, coordination, self-control, or attention that interfere with the ability to learn. The impairment is not related to a global deficiency of intelligence.
HP:0000407	Sensorineural hearing impairment	A type of hearing impairment in one or both ears related to an abnormal functionality of the cochlear nerve.
HP:0001270	Motor delay	A type of Developmental delay characterized by a delay in acquiring motor skills.
HP:0000510	Rod-cone dystrophy	An inherited retinal disease subtype in which the rod photoreceptors appear to be more severely affected than the cone photoreceptors. Typical presentation is with nyctalopia (due to rod dysfunction) followed by loss of mid-peripheral field of vision, which gradually extends and leaves many patients with a small central island of vision due to the preservation of macular cones.
HP:0000718	Aggressive behavior	Behavior or an act aimed at harming a person, animal, or physical property (e.g., acts of physical violence; shouting, swearing, and using harsh language; slashing someone's tires).
HP:0012450	Chronic constipation	Constipation for longer than three months with fewer than 3 bowel movements per week, straining, lumpy or hard stools, and a sensation of anorectal obstruction or incomplete defecation.
HP:0001166	Arachnodactyly	Abnormally long and slender fingers ("spider fingers").
HP:0000842	Hyperinsulinemia	An increased concentration of insulin in the blood.
HP:0011351	Moderate receptive language delay	A moderate delay in the acquisition of the ability to understand the speech of others.
HP:0002021	Pyloric stenosis	Pyloric stenosis, also known as infantile hypertrophic pyloric stenosis, is an uncommon condition in infants characterized by abnormal thickening of the pylorus muscles in the stomach leading to gastric outlet obstruction. Clinically infants are well at birth. Then, at 3 to 6 weeks of age, the infants present with projectile vomiting, potentially leading to dehydration and weight loss.
HP:0001631	Atrial septal defect	Atrial septal defect (ASD) is a congenital abnormality of the interatrial septum that enables blood flow between the left and right atria via the interatrial septum.
HP:0000750	Delayed speech and language development	A degree of language development that is significantly below the norm for a child of a specified age.
HP:0000077	Abnormality of the kidney	An abnormality of the kidney.
HP:0100702	Arachnoid cyst	An extra-parenchymal and intra-arachnoidal collection of fluid with a composition similar to that of cerebrospinal fluid.
HP:0001263	Global developmental delay	A delay in the achievement of motor or mental milestones in the domains of development of a child, including motor skills, speech and language, cognitive skills, and social and emotional skills. This term should only be used to describe children younger than five years of age.
HP:0000426	Prominent nasal bridge	Anterior positioning of the nasal root in comparison to the usual positioning for age.
HP:0000160	Narrow mouth	Distance between the commissures of the mouth more than 2 SD below the mean. Alternatively, an apparently decreased width of the oral aperture (subjective).
HP:0000104	Renal agenesis	Agenesis, that is, failure of the kidney to develop during embryogenesis and development.
HP:0011098	Speech apraxia	A type of apraxia that is characterized by difficulty or inability to execute speech movements because of problems with coordination and motor problems, leading to incorrect articulation. An increase of errors with increasing word and phrase length may occur.
HP:0001651	Dextrocardia	The heart is located in the right hand sided hemithorax. That is, there is a left-right reversal (or "mirror reflection") of the anatomical location of the heart in which the heart is locate on the right side instead of the left.
HP:0000093	Proteinuria	Increased levels of protein in the urine.
HP:0007018	Attention deficit hyperactivity disorder	Attention deficit hyperactivity disorder (ADHD) manifests at age 2-3 years or by first grade at the latest. The main symptoms are distractibility, impulsivity, hyperactivity, and often trouble organizing tasks and projects, difficulty going to sleep, and social problems from being aggressive, loud, or impatient.
HP:0001999	Abnormal facial shape	An abnormal morphology (form) of the face or its components.
HP:0012622	Chronic kidney disease	Functional anomaly of the kidney persisting for at least three months.
HP:0003074	Hyperglycemia	An increased concentration of glucose in the blood.
HP:0003468	Abnormal vertebral morphology	An abnormality of one or more of the vertebrae.
HP:0000316	Hypertelorism	Interpupillary distance more than 2 SD above the mean (alternatively, the appearance of an increased interpupillary distance or widely spaced eyes).
HP:0000300	Oval face	A face with a rounded and slightly elongated outline.
HP:0003396	Syringomyelia	Dilated, glial-lined cavity in spinal cord. This cavity does not communicate with the central canal, and usually is between the dorsal columns unilaterally or bilaterally along the side of the cord.
HP:0002591	Polyphagia	A neurological anomaly with gross overeating associated with an abnormally strong desire or need to eat.
HP:0002076	Migraine	Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms.
HP:0001627	Abnormal heart morphology	Any structural anomaly of the heart.
HP:0001363	Craniosynostosis	Craniosynostosis refers to the premature closure of the cranial sutures. Primary craniosynostosis refers to the closure of one or more sutures due to abnormalities in skull development, and secondary craniosynostosis results from failure of brain growth.
HP:0001332	Dystonia	An abnormally increased muscular tone that causes fixed abnormal postures. There is a slow, intermittent twisting motion that leads to exaggerated turning and posture of the extremities and trunk.
HP:0001256	Intellectual disability, mild	Mild intellectual disability is defined as an intelligence quotient (IQ) in the range of 50-69.

ATP2A1 NM_004320.6 Whole gene - Size : 26,061 bases

pLI : 0 LOEUF : 0.85 sHet : 0.005 pHaplo : 0.55 pTriplo : 0.37
Location : 28,889,726 - 28,915,787

Disease : Brody myopathy

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:108730 Orphanet:53347 HGNC:811 PMID:10914677 GTEx Portal Human Protein Atlas Ensembl

Human Phenotype Ontology Show/Hide

HP:0100284	EMG: myotonic discharges	High frequency discharges in electromyography (EMG) that vary in amplitude and frequency, waxing and waning continuously with firing frequencies ranging from 150/second down to 20/second and producing a sound that has been referred to as a dive bomber sound.
HP:0003623	Neonatal onset	Onset of signs or symptoms of disease within the first 28 days of life.
HP:0003710	Exercise-induced muscle cramps	Sudden and involuntary contractions of one or more muscles brought on by physical exertion.
HP:0001270	Motor delay	A type of Developmental delay characterized by a delay in acquiring motor skills.
HP:0002047	Malignant hyperthermia	Malignant hyperthermia is characterized by a rapid increase in temperature to 39-42 degrees C. Malignant hyperthermia may occur in response to either inhalational anesthetics such as halothane, to muscle relaxants such as succinylcholine, or to exercise.
HP:0001371	Flexion contracture	A flexion contracture is a bent (flexed) joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints.
HP:0001324	Muscle weakness	Reduced strength of muscles.
HP:0011463	Childhood onset	Onset of disease at the age of between 1 and 5 years.
HP:0003474	Somatic sensory dysfunction	An abnormality of the primary sensation that is mediated by peripheral nerves (pain, temperature, touch, vibration, joint position). The word hypoesthesia (or hypesthesia) refers to a reduction in cutaneous sensation to a specific type of testing.
HP:0031826	Abnormal reflex	Any anomaly of a reflex, i.e., of an automatic response mediated by the nervous system (a reflex does not need the intervention of conscious thought to occur).
HP:0002380	Fasciculations	Fasciculations are observed as small, local, involuntary muscle contractions (twitching) visible under the skin. Fasciculations result from increased irritability of an axon (which in turn is often a manifestation of disease of a motor neuron). This leads to sporadic discharges of all the muscle fibers controlled by the axon in isolation from other motor units.
HP:0003326	Myalgia	Pain in muscle.
HP:0002411	Myokymia	Myokymia consists of involuntary, fine, continuous, undulating contractions that spread across the affected striated muscle.
HP:0009046	Difficulty running	Reduced ability to run.
HP:0008967	Exercise-induced muscle stiffness	A type of muscle stiffness that occurs following physical exertion.
HP:0010548	Percussion myotonia	A localized myotonic contraction in a muscle in reaction to percussion (tapping with the examiner's finger, a rubber percussion hammer, or a similar object).
HP:0003712	Skeletal muscle hypertrophy	Abnormal increase in muscle size and mass not due to training.
HP:0000007	Autosomal recessive inheritance	A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals with two pathogenic alleles, either homozygotes (two copies of the same mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele).
HP:0002486	Myotonia	An involuntary and painless delay in the relaxation of skeletal muscle following contraction or electrical stimulation.

NFATC2IP NM_032815.4 Whole gene - Size : 16,285 bases

pLI : 0 LOEUF : 1.02 sHet : 0.015 pHaplo : 0.17 pTriplo : 0.66
Location : 28,962,128 - 28,978,413

Database :

DecipherGenomics OMIM:614525 GTEx Portal Human Protein Atlas Ensembl

ATXN2L NM_007245.4 Whole gene - Size : 14,238 bases

pLI : 1 LOEUF : 0.17 sHet : 0.387 pHaplo : 0.96 pTriplo : 0.98
Location : 28,834,320 - 28,848,558

Database :

DecipherGenomics PanelApp OMIM:607931 GTEx Portal Human Protein Atlas Ensembl

SPNS1 NM_032038.3 Whole gene - Size : 10,327 bases

pLI : 0.02 LOEUF : 0.6 sHet : 0.073 pHaplo : 0.07 pTriplo : 0.73
Location : 28,985,542 - 28,995,869

Database :

DecipherGenomics OMIM:612583 GTEx Portal Human Protein Atlas Ensembl

CD19 NM_001770.6 Whole gene - Size : 7,377 bases

pLI : 0.9 LOEUF : 0.35 sHet : 0.047 pHaplo : 0.4 pTriplo : 0.34
Location : 28,943,286 - 28,950,663

Disease : Common variable immunodeficiency

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:107265 Orphanet:1572 HGNC:1633 GTEx Portal Human Protein Atlas Ensembl

Human Phenotype Ontology Show/Hide

HP:0002633	Vasculitis	Inflammation of blood vessel.
HP:0002205	Recurrent respiratory infections	An increased susceptibility to respiratory infections as manifested by a history of recurrent respiratory infections.
HP:0002023	Anal atresia	Congenital absence of the anus, i.e., the opening at the bottom end of the intestinal tract.
HP:0002014	Diarrhea	Abnormally increased frequency (usually defined as three or more) loose or watery bowel movements a day.
HP:0002960	Autoimmunity	The occurrence of an immune reaction against the organism's own cells or tissues.
HP:0002829	Arthralgia	Joint pain.
HP:0002910	Elevated hepatic transaminase	Elevations of the levels of SGOT and SGPT in the serum. SGOT (serum glutamic oxaloacetic transaminase) and SGPT (serum glutamic pyruvic transaminase) are transaminases primarily found in the liver and heart and are released into the bloodstream as the result of liver or heart damage. SGOT and SGPT are used clinically mainly as markers of liver damage.
HP:0002837	Recurrent bronchitis	An increased susceptibility to bronchitis as manifested by a history of recurrent bronchitis.
HP:0002091	Restrictive ventilatory defect	A functional defect characterized by reduced total lung capacity (TLC) not associated with abnormalities of expiratory airflow or airway resistance. Spirometrically, a restrictive defect is defined as FEV1 (forced expiratory volume in 1 second) and FVC (forced vital capacity) less than 80 per cent. Restrictive lung disease may be caused by alterations in lung parenchyma or because of a disease of the pleura, chest wall, or neuromuscular apparatus.
HP:0002097	Emphysema
HP:0003621	Juvenile onset	Onset of signs or symptoms of disease between the age of 5 and 15 years.
HP:0001878	Hemolytic anemia	A type of anemia caused by premature destruction of red blood cells (hemolysis).
HP:0011839	Abnormal T cell count	A deviation from the normal count of T cells.
HP:0011108	Recurrent sinusitis	A recurrent form of sinusitis.
HP:0000007	Autosomal recessive inheritance	A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals with two pathogenic alleles, either homozygotes (two copies of the same mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele).
HP:0002718	Recurrent bacterial infections	Increased susceptibility to bacterial infections, as manifested by recurrent episodes of bacterial infection.
HP:0002721	Immunodeficiency	Failure of the immune system to protect the body adequately from infection, due to the absence or insufficiency of some component process or substance.
HP:0030388	Decreased proportion of class-switched memory B cells	A reduction in the normal proportion of class-switched memory B cells (CD19+/CD27+/IgM+/IgD+) relative to the total number of B cells. Marginal zone B cells undergo limited somatic hypermutation and produce high-affinity IgM and some IgG, whereas class-switched memory B cells synthetize IgG, IgM, and IgA.
HP:0006783	Posterior pharyngeal cleft
HP:0002850	Decreased circulating total IgM	An abnormally decreased level of immunoglobulin M (IgM) in blood.
HP:0000006	Autosomal dominant inheritance	A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele.
HP:0001744	Splenomegaly	Abnormal increased size of the spleen.
HP:0000388	Otitis media	Inflammation or infection of the middle ear.
HP:0002729	Follicular hyperplasia	Lymphadenopathy (enlargement of lymph nodes) owing to hyperplasia of follicular (germinal) centers.
HP:0001287	Meningitis	Inflammation of the meninges.
HP:0005387	Combined immunodeficiency	A group of phenotypically heterogeneous genetic disorders characterized by profound deficiencies of T- and B-cell function, which predispose the patients to both infectious and noninfectious complications.
HP:0005435	Impaired T cell function	Abnormally reduced ability of T cells to perform their functions in cell-mediated immunity.
HP:0000248	Brachycephaly	An abnormality of skull shape characterized by a decreased anterior-posterior diameter. That is, a cephalic index greater than 81%. Alternatively, an apparently shortened anteroposterior dimension (length) of the head compared to width.
HP:0002716	Lymphadenopathy	Enlargment (swelling) of a lymph node.
HP:0000389	Chronic otitis media	Chronic otitis media refers to fluid, swelling, or infection of the middle ear that does not heal and may cause permanent damage to the ear.
HP:0003593	Infantile onset	Onset of signs or symptoms of disease between 28 days to one year of life.
HP:0001392	Abnormality of the liver	An abnormality of the liver.
HP:0032139	Reduced isohemagglutinin level	Level of isohemagglutinin reduced below expected concentration. An isohemagglutinin refers to the naturally occurring antibodies in the ABO blood group system (i.e., anti-A in a group B person, anti-B in a group A person, and anti-A, anti-B, and anti-A,B in a group O person).
HP:0004313	Decreased circulating antibody level	An abnormally decreased level of immunoglobulin in blood.
HP:0002090	Pneumonia	Inflammation of any part of the lung parenchyma.
HP:0032134	Chronic decreased circulating total IgG	A lasting reduction beneath the normal level of total immunoglobulin G (IgG) in the blood.
HP:0100723	Gastrointestinal stroma tumor
HP:0410301	Partial absence of specific antibody response to unconjugated pneumococcus vaccine	A reduced ability to synthesize postvaccination antibodies against a pneumococcus antigen, as measured by antibody titer determination following vaccination.
HP:0000403	Recurrent otitis media	Increased susceptibility to otitis media, as manifested by recurrent episodes of otitis media.
HP:0002720	Decreased circulating IgA level	Decreased levels of immunoglobulin A (IgA).
HP:0002664	Neoplasm	An organ or organ-system abnormality that consists of uncontrolled autonomous cell-proliferation which can occur in any part of the body as a benign or malignant neoplasm (tumor).
HP:0001973	Autoimmune thrombocytopenia	The presence of thrombocytopenia in combination with detection of antiplatelet antibodies.
HP:0001531	Failure to thrive in infancy
HP:0002110	Bronchiectasis	Persistent abnormal dilatation of the bronchi owing to localized and irreversible destruction and widening of the large airways.
HP:0002240	Hepatomegaly	Abnormally increased size of the liver.
HP:0011463	Childhood onset	Onset of disease at the age of between 1 and 5 years.
HP:0000509	Conjunctivitis	Inflammation of the conjunctiva.
HP:0002665	Lymphoma	A cancer originating in lymphocytes and presenting as a solid tumor of lymhpoid cells.
HP:0001888	Lymphopenia	A reduced number of lymphocytes in the blood.
HP:0000979	Purpura	Purpura (from Latin: purpura, meaning "purple") is the appearance of red or purple discolorations on the skin that do not blanch on applying pressure. They are caused by bleeding underneath the skin. This term refers to an abnormally increased susceptibility to developing purpura. Purpura are larger than petechiae.
HP:0004315	Decreased circulating IgG level	An abnormally decreased level of immunoglobulin G (IgG) in blood.
HP:0010975	Abnormal B cell count	A deviation from the normal count of B cells, i.e., the cells that are formed in the bone marrow, migrate to the peripheral lymphatic system, and mature into plasma cells or memory cells.
HP:0006532	Recurrent pneumonia	An increased susceptibility to pneumonia as manifested by a history of recurrent episodes of pneumonia.

LAT NM_001014987.2 Whole gene - Size : 5,958 bases

pLI : 0.02 LOEUF : 0.67 sHet : 0.042 pHaplo : 0.17 pTriplo : 0.43
Location : 28,996,147 - 29,002,105

Disease : Severe combined immunodeficiency due to LAT deficiency

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:602354 Orphanet:504523 HGNC:18874 PMID:27522155 GTEx Portal Human Protein Atlas Ensembl

Human Phenotype Ontology Show/Hide

HP:0011968	Feeding difficulties	Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it.
HP:0002395	Lower limb hyperreflexia
HP:0025335	Delayed ability to stand	A failure to achieve the ability to stand up at an appropriate developmental stage. Most children begin to walk alone at 11 to 15 months of age. On average, children can stand while holding on at the age of 9 to 10 months, can pull up to stand and walk with one hand being held at 12 months, and can stand alone and walk well at 18 months.
HP:0031936	Delayed ability to walk	A failure to achieve the ability to walk at an appropriate developmental stage. Most children learn to walk in a series of stages, and learn to walk short distances independently between 12 and 15 months.
HP:0025331	Upgaze palsy	A limitation of the ability to direct one's gaze above the horizontal meridian.
HP:0002454	Eye of the tiger anomaly of globus pallidus	The presence, on T2-weighted magnetic resonance imaging, of markedly low signal intensity of the globus pallidus that surrounds a central region of high signal intensity in the anteromedial globus pallidus, producing an eye-of-the-tiger appearance. The sign is thought to represent iron accumulation in the globus pallidus.
HP:0000739	Anxiety	Intense feelings of nervousness, tension, or panic often arise in response to interpersonal stresses. There is worry about the negative effects of past unpleasant experiences and future negative possibilities. Individuals may feel fearful, apprehensive, or threatened by uncertainty, and they may also have fears of falling apart or losing control.
HP:0007994	Peripheral visual field loss	Loss of peripheral vision with retention of central vision, resulting in a constricted circular tunnel-like field of vision.
HP:0000657	Oculomotor apraxia	Ocular motor apraxia is a deficiency in voluntary, horizontal, lateral, fast eye movements (saccades) with retention of slow pursuit movements. The inability to follow objects visually is often compensated by head movements. There may be decreased smooth pursuit, and cancellation of the vestibulo-ocular reflex.
HP:0001288	Gait disturbance	The term gait disturbance can refer to any disruption of the ability to walk. In general, this can refer to neurological diseases but also fractures or other sources of pain that is triggered upon walking. However, in the current context gait disturbance refers to difficulty walking on the basis of a neurological or muscular disease.
HP:0000708	Atypical behavior	Atypical behavior is an abnormality in a person's actions, which can be controlled or modulated by the will of the individual. While abnormal behaviors can be difficult to control, they are distinct from other abnormal actions that cannot be affected by the individual's will.
HP:0005656	Positional foot deformity	A foot deformity resulting due to an abnormality affecting the muscle and soft tissue. In contrast if the bones of the foot are affected the term structural foot deformity applies.
HP:0020045	Esodeviation	A manifest or latent ocular deviation in which one or both eyes tends to deviate nasally.
HP:0001348	Brisk reflexes	Tendon reflexes that are noticeably more active than usual (conventionally denoted 3+ on clinical examination). Brisk reflexes may or may not indicate a neurological lesion. They are distinguished from hyperreflexia by the fact that hyerreflexia is characterized by hyperactive repeating (clonic) reflexes, which are considered to be always abnormal.
HP:0002928	Decreased activity of the pyruvate dehydrogenase complex
HP:0000508	Ptosis	The upper eyelid margin is positioned 3 mm or more lower than usual and covers the superior portion of the iris (objective); or, the upper lid margin obscures at least part of the pupil (subjective).
HP:0002136	Broad-based gait	An abnormal gait pattern in which persons stand and walk with their feet spaced widely apart. This is often a component of cerebellar ataxia.
HP:0000252	Microcephaly	Head circumference below 2 standard deviations below the mean for age and gender.
HP:0000007	Autosomal recessive inheritance	A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals with two pathogenic alleles, either homozygotes (two copies of the same mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele).
HP:0001266	Choreoathetosis	Involuntary movements characterized by both athetosis (inability to sustain muscles in a fixed position) and chorea (widespread jerky arrhythmic movements).
HP:0001319	Neonatal hypotonia	Muscular hypotonia (abnormally low muscle tone) manifesting in the neonatal period.
HP:0002194	Delayed gross motor development	A type of motor delay characterized by a delay in acquiring the ability to control the large muscles of the body for walking, running, sitting, and crawling.
HP:0012379	Abnormal circulating enzyme concentration or activity	Concentration or activity of an enzyme is above or below the limits of normal in the blood circulation.
HP:0003487	Babinski sign	Upturning of the big toe (and sometimes fanning of the other toes) in response to stimulation of the sole of the foot. If the Babinski sign is present it can indicate damage to the corticospinal tract.
HP:0002465	Poor speech
HP:0001251	Ataxia	Cerebellar ataxia refers to ataxia due to dysfunction of the cerebellum. This causes a variety of elementary neurological deficits including asynergy (lack of coordination between muscles, limbs and joints), dysmetria (lack of ability to judge distances that can lead to under- or overshoot in grasping movements), and dysdiadochokinesia (inability to perform rapid movements requiring antagonizing muscle groups to be switched on and off repeatedly).
HP:0031960	Arm dystonia	A type of dystonia (abnormally increased muscular tone causing fixed abnormal postures) that affects muscles of the arms.
HP:0500231	Abnormal CSF pyruvate family amino acid concentration	Any deviation from the normal concentration of pyruvate-family amino acids in the cerebrospinal fluid.
HP:0002307	Drooling	Habitual flow of saliva out of the mouth.
HP:0000639	Nystagmus	Rhythmic, involuntary oscillations of one or both eyes related to abnormality in fixation, conjugate gaze, or vestibular mechanisms.
HP:0000707	Abnormality of the nervous system	An abnormality of the nervous system.
HP:0012043	Pendular nystagmus	Rhythmic, involuntary sinusoidal oscillations of one or both eyes. The waveform of pendular nystagmus may occur in any direction.
HP:0003128	Lactic acidosis	An abnormal buildup of lactic acid in the body, leading to acidification of the blood and other bodily fluids.
HP:0002180	Neurodegeneration	Progressive loss of neural cells and tissue.
HP:0001252	Hypotonia	Hypotonia is an abnormally low muscle tone (the amount of tension or resistance to movement in a muscle). Even when relaxed, muscles have a continuous and passive partial contraction which provides some resistance to passive stretching. Hypotonia thus manifests as diminished resistance to passive stretching. Hypotonia is not the same as muscle weakness, although the two conditions can co-exist.
HP:0100503	Low levels of vitamin B1	A reduced concentration of vitamin B1.
HP:0010864	Intellectual disability, severe	Severe mental retardation is defined as an intelligence quotient (IQ) in the range of 20-34.
HP:0000726	Dementia	A loss of global cognitive ability of sufficient amount to interfere with normal social or occupational function. Dementia represents a loss of previously present cognitive abilities, generally in adults, and can affect memory, thinking, language, judgment, and behavior.
HP:0003593	Infantile onset	Onset of signs or symptoms of disease between 28 days to one year of life.
HP:0001270	Motor delay	A type of Developmental delay characterized by a delay in acquiring motor skills.
HP:0001260	Dysarthria	Dysarthric speech is a general description referring to a neurological speech disorder characterized by poor articulation. Depending on the involved neurological structures, dysarthria may be further classified as spastic, flaccid, ataxic, hyperkinetic and hypokinetic, or mixed.
HP:0002355	Difficulty walking	Reduced ability to walk (ambulate).
HP:0002268	Paroxysmal dystonia	A form of dystonia characterized by episodes of dystonia (often hemidystonia or generalized) lasting from minutes to hours. There are no dystonic symptoms between episodes.
HP:0001263	Global developmental delay	A delay in the achievement of motor or mental milestones in the domains of development of a child, including motor skills, speech and language, cognitive skills, and social and emotional skills. This term should only be used to describe children younger than five years of age.
HP:0011098	Speech apraxia	A type of apraxia that is characterized by difficulty or inability to execute speech movements because of problems with coordination and motor problems, leading to incorrect articulation. An increase of errors with increasing word and phrase length may occur.
HP:0000496	Abnormality of eye movement	An abnormality in voluntary or involuntary eye movements or their control.
HP:0032988	Persistent head lag	The Premie-Neuro and the Dubowitz Neurological Examination score head lag in the same manner. Scoring for both is as follows: 0 = head drops and stays back, 1 = tries to lift head but drops it back, 2 = able to lift head slightly, 3 = lifts head in line with body, and 4 = head in front of body. This term applies if head lag persists beyond an expected age at a level of 0 or 1. Persistent head lag beyond age 4 mo has been linked to poor outcomes.
HP:0000486	Strabismus	A misalignment of the eyes so that the visual axes deviate from bifoveal fixation. The classification of strabismus may be based on a number of features including the relative position of the eyes, whether the deviation is latent or manifest, intermittent or constant, concomitant or otherwise and according to the age of onset and the relevance of any associated refractive error.
HP:0004302	Functional motor deficit
HP:0007325	Generalized dystonia	A type of dystonia that affects all or most of the body.
HP:0000546	Retinal degeneration	A nonspecific term denoting degeneration of the retinal pigment epithelium and/or retinal photoreceptor cells.
HP:0001332	Dystonia	An abnormally increased muscular tone that causes fixed abnormal postures. There is a slow, intermittent twisting motion that leads to exaggerated turning and posture of the extremities and trunk.
HP:0006961	Jerky head movements
HP:0001256	Intellectual disability, mild	Mild intellectual disability is defined as an intelligence quotient (IQ) in the range of 50-69.
HP:0001276	Hypertonia	A condition in which there is increased muscle tone so that arms or legs, for example, are stiff and difficult to move.
HP:0031139	Frog-leg posture	A type of rest posture in an infant that indicated a generalized reduction in muscle tone. The hips are flexed and the legs are abducted to an extent that causes the lateral thigh to rest upon the supporting surface. This posture is said to resemble the legs of a frog.
HP:0001347	Hyperreflexia	Hyperreflexia is the presence of hyperactive stretch reflexes of the muscles.

TUFM NM_003321.5 Whole gene - Size : 3,937 bases

pLI : 0 LOEUF : 0.74 sHet : 0.022 pHaplo : 0.17 pTriplo : 0.89
Location : 28,853,732 - 28,857,669

Disease : Combined oxidative phosphorylation defect type 4

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:602389 Orphanet:254925 HGNC:12420 PMID:17160893 GTEx Portal Human Protein Atlas Ensembl

Human Phenotype Ontology Show/Hide

HP:0003593	Infantile onset	Onset of signs or symptoms of disease between 28 days to one year of life.
HP:0002240	Hepatomegaly	Abnormally increased size of the liver.
HP:0001942	Metabolic acidosis	Metabolic acidosis (MA) is characterized by a fall in blood pH due to a reduction of serum bicarbonate concentration. This can occur as a result of either the accumulation of acids (high anion gap MA) or the loss of bicarbonate from the gastrointestinal tract or the kidney (hyperchloremic MA). By definition, MA is not due to a respirary cause.
HP:0002151	Increased serum lactate	Abnormally increased level of blood lactate (2-hydroxypropanoic acid). Lactate is produced from pyruvate by lactate dehydrogenase during normal metabolism. The terms lactate and lactic acid are often used interchangeably but lactate (the component measured in blood) is strictly a weak base whereas lactic acid is the corresponding acid. Lactic acidosis is often used clinically to describe elevated lactate but should be reserved for cases where there is a corresponding acidosis (pH below 7.35).
HP:0002415	Leukodystrophy	Leukodystrophy refers to deterioration of white matter of the brain resulting from degeneration of myelin sheaths in the CNS. Their basic defect is directly related to the synthesis and maintenance of myelin membranes. Symmetric white matter involvement at MRI is a typical finding in patients with leukodystrophies.
HP:0001298	Encephalopathy	Encephalopathy is a term that means brain disease, damage, or malfunction. In general, encephalopathy is manifested by an altered mental state.
HP:0000639	Nystagmus	Rhythmic, involuntary oscillations of one or both eyes related to abnormality in fixation, conjugate gaze, or vestibular mechanisms.
HP:0002179	Opisthotonus
HP:0001987	Hyperammonemia	An increased concentration of ammonia in the blood.
HP:0002376	Developmental regression	Loss of developmental skills, as manifested by loss of developmental milestones.
HP:0003128	Lactic acidosis	An abnormal buildup of lactic acid in the body, leading to acidification of the blood and other bodily fluids.
HP:0002126	Polymicrogyria	Polymicrogyria is a congenital malformation of the cerebral cortex characterized by abnormal cortical layering (lamination) and an excessive number of small gyri (folds).
HP:0001522	Death in infancy	Death within the first 24 months of life.
HP:0000252	Microcephaly	Head circumference below 2 standard deviations below the mean for age and gender.
HP:0000007	Autosomal recessive inheritance	A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals with two pathogenic alleles, either homozygotes (two copies of the same mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele).
HP:0001319	Neonatal hypotonia	Muscular hypotonia (abnormally low muscle tone) manifesting in the neonatal period.
HP:0001511	Intrauterine growth retardation	An abnormal restriction of fetal growth with fetal weight below the tenth percentile for gestational age.
HP:0002878	Respiratory failure	A severe form of respiratory insufficiency characterized by inadequate gas exchange such that the levels of oxygen or carbon dioxide cannot be maintained within normal limits.
HP:0001257	Spasticity	A motor disorder characterized by a velocity-dependent increase in tonic stretch reflexes with increased muscle tone, exaggerated (hyperexcitable) tendon reflexes.

17 Non-OMIM Gene overlap(s)

ENSG00000261067
Size : 15,971 bases

Location : 28,986,125 - 29,002,096

ENSG00000251417
Size : 15,085 bases

Location : 28,814,064 - 28,829,149

NFATC2IP-AS1
Size : 14,067 bases

Location : 28,964,137 - 28,978,204

NPIPB10P
Size : 14,071 bases

pLI : 0.1 LOEUF : 1.88
Location : 29,049,976 - 29,064,047

ENSG00000260570
Size : 6,588 bases

Location : 28,841,933 - 28,848,521

ENSG00000260367
Size : 4,862 bases

Location : 28,985,283 - 28,990,145

ENSG00000278528
Size : 3,710 bases

Location : 28,785,145 - 28,788,855

ENSG00000240634
Size : 693 bases

Location : 28,825,301 - 28,825,994

ENSG00000260796
Size : 1,463 bases

Location : 28,831,891 - 28,833,354

ENSG00000275807
Size : 1,538 bases

Location : 28,833,752 - 28,835,290

ENSG00000261766
Size : 1,174 bases

Location : 28,873,487 - 28,874,661

ATP2A1-AS1
Size : 2,000 bases

Location : 28,889,259 - 28,891,259

ENSG00000261552
Size : 1,638 bases

Location : 29,000,461 - 29,002,099

NOVEL
Size : 103 bases

Location : 28,797,731 - 28,797,834

KNOWN
Size : 88 bases

Location : 28,855,240 - 28,855,328

NOVEL
Size : 127 bases

Location : 28,892,801 - 28,892,928

KNOWN
Size : 78 bases

Location : 28,969,904 - 28,969,982

34 ClinGen CNV overlap(s) (>= 70% only)

0 Benign CNV 0 Likely benign CNV 0 Uncertain CNV 2 Likely pathogenic CNV 31 Pathogenic CNV

#1 Pathogenic (16p11.2)
Location : 28,802,396 - 29,051,191 | Size : 248,795 bases

Score : 1

Mean Coverage : 95 %

#2 Pathogenic (16p11.2)
Location : 28,763,833 - 29,051,191 | Size : 287,358 bases

Score : 0

Mean Coverage : 94 %

#3 Pathogenic (16p11.2)
Location : 28,763,834 - 29,051,191 | Size : 287,357 bases

Score : 1

Mean Coverage : 94 %

#4 Pathogenic (nssv13644823)
Location : 28,763,833 - 29,043,863 | Size : 280,030 bases

Score : 0

Mean Coverage : 93 %

#5 Pathogenic (16p11.2)
Location : 28,747,519 - 29,051,191 | Size : 303,672 bases

Score : 1

Mean Coverage : 92 %

#6 Pathogenic (16p11.2)
Location : 28,819,027 - 29,051,191 | Size : 232,164 bases

Score : 0

Mean Coverage : 92 %

#7 Pathogenic (nssv3397222)
Location : 28,819,027 - 29,051,191 | Size : 232,164 bases

Score : 0

Mean Coverage : 92 %

#8 Pathogenic (nssv13652140)
Location : 28,819,027 - 29,043,972 | Size : 224,945 bases

Score : 0

Mean Coverage : 90 %

#9 Pathogenic (nssv1609384)
Location : 28,820,742 - 29,044,776 | Size : 224,034 bases

Score : 0

Mean Coverage : 90 %

#10 Pathogenic (nssv1610312)
Location : 28,824,793 - 29,044,776 | Size : 219,983 bases

Score : 0

Mean Coverage : 89 %

#11 Pathogenic (nssv1604382)
Location : 28,824,793 - 29,043,960 | Size : 219,167 bases

Score : 0

Mean Coverage : 89 %

#12 Pathogenic (16p11.2)
Location : 28,825,604 - 29,043,450 | Size : 217,846 bases

Score : 1

Mean Coverage : 89 %

#13 Pathogenic (16p11.2)
Location : 28,826,161 - 29,043,960 | Size : 217,799 bases

Score : 1

Mean Coverage : 89 %

#14 Pathogenic (nssv1609601)
Location : 28,733,738 - 29,044,776 | Size : 311,038 bases

Score : 0

Mean Coverage : 88 %

#15 Pathogenic (16p11.2)
Location : 28,734,570 - 29,043,450 | Size : 308,880 bases

Score : 1
Phenotype : Distal 16p11.2 microdeletion syndrome

Mean Coverage : 88 %

#16 Pathogenic/Likely pathogenic (nssv13642995)
Location : 28,826,161 - 29,043,901 | Size : 217,740 bases

Score : 0

Mean Coverage : 88 %

#17 Pathogenic (nssv3396771)
Location : 28,708,172 - 29,051,191 | Size : 343,019 bases

Score : 0

Mean Coverage : 86 %

#18 Pathogenic (nssv577891)
Location : 28,721,798 - 29,037,107 | Size : 315,309 bases

Score : 1

Mean Coverage : 85 %

#19 Pathogenic (Single allele)
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Score : 1
Phenotype : Proximal 16p11.2 microdeletion syndrome

Mean Coverage : 85 %

#20 Pathogenic (nssv578114)
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Score : 1

Mean Coverage : 85 %

#21 Pathogenic (16p11.2)
Location : 28,837,904 - 29,088,624 | Size : 250,720 bases

Score : 0

Mean Coverage : 85 %

#22 Pathogenic (16p11.2)
Location : 28,689,084 - 29,051,191 | Size : 362,107 bases

Score : 0
Phenotype : Distal 16p11.2 microdeletion syndrome

Mean Coverage : 83 %

#23 Pathogenic (16p11.2)
Location : 28,689,084 - 29,051,191 | Size : 362,107 bases

Score : 0

Mean Coverage : 83 %

#24 Pathogenic (nssv1610483)
Location : 28,689,084 - 29,051,191 | Size : 362,107 bases

Score : 0

Mean Coverage : 83 %

#25 Likely pathogenic (nssv1415448)
Location : 28,824,793 - 29,133,735 | Size : 308,942 bases

Score : 0

Mean Coverage : 81 %

#26 Pathogenic (nssv1603731)
Location : 28,843,753 - 29,031,071 | Size : 187,318 bases

Score : 0

Mean Coverage : 81 %

#27 Pathogenic (nssv578225)
Location : 28,854,628 - 29,037,107 | Size : 182,479 bases

Score : 1

Mean Coverage : 80 %

#28 Pathogenic (nssv1415380)
Location : 28,861,530 - 29,043,960 | Size : 182,430 bases

Score : 0

Mean Coverage : 80 %

#29 Pathogenic (16p11.2)
Location : 28,784,626 - 29,230,353 | Size : 445,727 bases

Score : 1
Phenotype : Distal 16p11.2 microdeletion syndrome

Mean Coverage : 76 %

#30 Pathogenic (16p11.2)
Location : 28,819,027 - 28,988,225 | Size : 169,198 bases

Score : 0

Mean Coverage : 76 %

#31 Pathogenic (16p11.2)
Location : 28,861,530 - 29,031,059 | Size : 169,529 bases

Score : 1
Phenotype : Macular dystrophy,Intellectual disability,moderate

Mean Coverage : 76 %

#32 Pathogenic (nssv707120)
Location : 28,861,530 - 29,031,059 | Size : 169,529 bases

Score : 0

Mean Coverage : 76 %

#33 Likely pathogenic (Single allele)
Location : 28,668,058 - 29,001,338 | Size : 333,280 bases

Score : 1
Phenotype : Proximal 16p11.2 microdeletion syndrome

Mean Coverage : 71 %

#34 Pathogenic (g.)
Location : 28,854,295 - 29,001,333 | Size : 147,038 bases

Score : 1
Phenotype : Brody myopathy

Mean Coverage : 70 %

86 Decipher CNV overlap(s) (>= 70% only)

0 Benign CNV 43 Unknown CNV 10 Uncertain CNV 33 Pathogenic CNV

#1 : pathogenic
Location : 28,796,367 - 29,076,269 | Size : 279,902 bases

Patient Id : 331026
Gender : Inconnu
Phenotype : Global developmental delay

Mean Coverage : 95 %

#2 : pathogenic
Location : 28,796,367 - 29,076,269 | Size : 279,902 bases

Patient Id : 331703
Gender : Inconnu
Phenotype : Autism, Obesity, Hypercholesterolemia, Autism, Obesity, Hypercholesterolemia

Mean Coverage : 95 %

#3 : pathogenic
Location : 28,748,615 - 29,051,191 | Size : 302,576 bases

Patient Id : 376144
Gender : Inconnu
Phenotype : Intellectual disability, mild, Laryngomalacia, Intellectual disability, mild, Laryngomalacia

Mean Coverage : 92 %

#4 : unknown
Location : 28,819,027 - 29,051,191 | Size : 232,164 bases

Patient Id : 268970
Gender : Inconnu

Mean Coverage : 92 %

#5 : pathogenic
Location : 28,824,856 - 29,051,191 | Size : 226,335 bases

Patient Id : 353972
Gender : Inconnu
Phenotype : Global developmental delay

Mean Coverage : 90 %

#6 : unknown
Location : 28,823,914 - 29,043,863 | Size : 219,949 bases

Patient Id : 256834
Gender : Inconnu
Phenotype : Acanthosis nigricans, Obesity

Mean Coverage : 89 %

#7 : unknown
Location : 28,824,793 - 29,044,776 | Size : 219,983 bases

Patient Id : 265791
Gender : Inconnu

Mean Coverage : 89 %

#8 : unknown
Location : 28,824,793 - 29,044,776 | Size : 219,983 bases

Patient Id : 266893
Gender : Inconnu

Mean Coverage : 89 %

#9 : unknown
Location : 28,824,793 - 29,044,776 | Size : 219,983 bases

Patient Id : 267633
Gender : Inconnu

Mean Coverage : 89 %

#10 : unknown
Location : 28,824,793 - 29,044,716 | Size : 219,923 bases

Patient Id : 249980
Gender : Inconnu
Phenotype : Narrow palate, Epicanthus, Long philtrum, Abnormality of the outer ear, Strabismus, Periorbital fullness, Hyperactivity, Intellectual disability, Seizure, Macrodontia, Preauricular pit

Mean Coverage : 89 %

#11 : uncertain
Location : 28,824,777 - 29,039,612 | Size : 214,835 bases

Patient Id : 288223
Gender : Inconnu
Phenotype : Autism, Obesity

Mean Coverage : 88 %

#12 : uncertain
Location : 28,824,777 - 29,039,612 | Size : 214,835 bases

Patient Id : 289170
Gender : Inconnu
Phenotype : Intrauterine growth retardation, Anal atresia

Mean Coverage : 88 %

#13 : uncertain
Location : 28,824,777 - 29,039,612 | Size : 214,835 bases

Patient Id : 289489
Gender : Inconnu
Phenotype : Behavioral abnormality, Intellectual disability

Mean Coverage : 88 %

#14 : uncertain
Location : 28,824,777 - 29,039,612 | Size : 214,835 bases

Patient Id : 290435
Gender : Inconnu
Phenotype : Seizure, Schizophrenia

Mean Coverage : 88 %

#15 : pathogenic
Location : 28,824,777 - 29,039,612 | Size : 214,835 bases

Patient Id : 331214
Gender : Inconnu
Phenotype : Global developmental delay

Mean Coverage : 88 %

#16 : pathogenic
Location : 28,824,777 - 29,039,612 | Size : 214,835 bases

Patient Id : 331402
Gender : Inconnu
Phenotype : Autism, Intellectual disability

Mean Coverage : 88 %

#17 : pathogenic
Location : 28,824,777 - 29,039,612 | Size : 214,835 bases

Patient Id : 331410
Gender : Inconnu
Phenotype : Global developmental delay

Mean Coverage : 88 %

#18 : unknown
Location : 28,824,777 - 29,084,776 | Size : 259,999 bases

Patient Id : 251690
Gender : Inconnu
Phenotype : Intellectual disability, Intellectual disability, Intellectual disability

Mean Coverage : 88 %

#19 : pathogenic
Location : 28,824,793 - 29,042,059 | Size : 217,266 bases

Patient Id : 318160
Gender : Inconnu

Mean Coverage : 88 %

#20 : pathogenic
Location : 28,824,793 - 29,042,059 | Size : 217,266 bases

Patient Id : 358409
Gender : Inconnu

Mean Coverage : 88 %

#21 : unknown
Location : 28,824,793 - 29,042,118 | Size : 217,325 bases

Patient Id : 267549
Gender : Inconnu
Phenotype : Abnormality of the face, Strabismus, Intellectual disability

Mean Coverage : 88 %

#22 : unknown
Location : 28,824,793 - 29,042,118 | Size : 217,325 bases

Patient Id : 277574
Gender : Inconnu
Phenotype : Autistic behavior, Increased body weight, Moderate global developmental delay, Proportionate tall stature, Autistic behavior, Increased body weight, Moderate global developmental delay, Proportionate tall stature, Autistic behavior, Increased body weight, Moderate global developmental delay, Proportionate tall stature

Mean Coverage : 88 %

#23 : pathogenic
Location : 28,824,793 - 29,042,118 | Size : 217,325 bases

Patient Id : 339899
Gender : Inconnu
Phenotype : Intellectual disability, mild, Obesity

Mean Coverage : 88 %

#24 : uncertain
Location : 28,824,793 - 29,042,118 | Size : 217,325 bases

Patient Id : 368772
Gender : Inconnu
Phenotype : Intellectual disability

Mean Coverage : 88 %

#25 : pathogenic
Location : 28,824,801 - 29,040,571 | Size : 215,770 bases

Patient Id : 411578
Gender : Inconnu
Phenotype : Strabismus, Global developmental delay, Generalized hypotonia, Obesity, Short foot, Polyphagia, Genu varum, Small hand, Strabismus, Global developmental delay, Generalized hypotonia, Obesity, Short foot, Polyphagia, Genu varum, Small hand

Mean Coverage : 88 %

#26 : pathogenic
Location : 28,825,604 - 29,042,014 | Size : 216,410 bases

Patient Id : 394779
Gender : Inconnu
Phenotype : Intellectual disability, Hypotonia

Mean Coverage : 88 %

#27 : pathogenic
Location : 28,833,435 - 29,046,284 | Size : 212,849 bases

Patient Id : 282629
Gender : Inconnu
Phenotype : Short philtrum, Posteriorly rotated ears, Anteverted nares, Strabismus, Hypotelorism, Aggressive behavior, Anxiety, Delayed speech and language development, Obesity, Frontal bossing, Gastroesophageal reflux, Secondary microcephaly, Attention deficit hyperactivity disorder

Mean Coverage : 87 %

#28 : pathogenic
Location : 28,833,435 - 29,046,284 | Size : 212,849 bases

Patient Id : 285165
Gender : Inconnu
Phenotype : Depression, Obesity

Mean Coverage : 87 %

#29 : unknown
Location : 28,823,913 - 29,103,019 | Size : 279,106 bases

Patient Id : 277713
Gender : Inconnu
Phenotype : Abnormality of the nervous system, Seizure, Overgrowth, Intellectual disability, borderline, Abnormal CNS myelination

Mean Coverage : 86 %

#30 : unknown
Location : 28,824,793 - 29,031,059 | Size : 206,266 bases

Patient Id : 270628
Gender : Inconnu
Phenotype : Tall stature, Intellectual disability, Obesity

Mean Coverage : 86 %

#31 : uncertain
Location : 28,824,793 - 29,031,059 | Size : 206,266 bases

Patient Id : 377611
Gender : Inconnu
Phenotype : Intellectual disability, Global developmental delay, Intellectual disability, Global developmental delay

Mean Coverage : 86 %

#32 : pathogenic
Location : 28,824,793 - 29,031,059 | Size : 206,266 bases

Patient Id : 383006
Gender : Inconnu

Mean Coverage : 86 %

#33 : unknown
Location : 28,837,249 - 29,042,259 | Size : 205,010 bases

Patient Id : 249363
Gender : Inconnu
Phenotype : Preauricular skin tag, Ptosis, Delayed speech and language development, Intellectual disability, Hypotonia, Feeding difficulties in infancy

Mean Coverage : 86 %

#34 : unknown
Location : 28,837,389 - 29,042,178 | Size : 204,789 bases

Patient Id : 277182
Gender : Inconnu
Phenotype : Ptosis, Epicanthus inversus, Blepharophimosis, Global developmental delay

Mean Coverage : 85 %

#35 : pathogenic
Location : 28,837,389 - 29,042,178 | Size : 204,789 bases

Patient Id : 300646
Gender : Inconnu
Phenotype : Stereotypy, Global developmental delay, Absent speech

Mean Coverage : 85 %

#36 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 250064
Gender : Inconnu
Phenotype : Abnormality of the face, Intellectual disability

Mean Coverage : 85 %

#37 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 251199
Gender : Inconnu
Phenotype : Intellectual disability, Obesity

Mean Coverage : 85 %

#38 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 253267
Gender : Inconnu
Phenotype : Microcephaly, Intellectual disability, Nasal speech, Microcephaly, Intellectual disability, Nasal speech, Microcephaly, Intellectual disability, Nasal speech

Mean Coverage : 85 %

#39 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 293080
Gender : Inconnu
Phenotype : Obesity, Cognitive impairment, Obesity, Cognitive impairment, Obesity, Cognitive impairment

Mean Coverage : 85 %

#40 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 301697
Gender : Inconnu
Phenotype : Autism, Cognitive impairment, Autism, Cognitive impairment

Mean Coverage : 85 %

#41 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 303558
Gender : Inconnu

Mean Coverage : 85 %

#42 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 276681
Gender : Inconnu
Phenotype : Global developmental delay

Mean Coverage : 85 %

#43 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 278593
Gender : Inconnu
Phenotype : Intellectual disability, moderate

Mean Coverage : 85 %

#44 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 284131
Gender : Inconnu
Phenotype : Autistic behavior

Mean Coverage : 85 %

#45 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 287726
Gender : Inconnu
Phenotype : Global developmental delay, Global developmental delay

Mean Coverage : 85 %

#46 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 292839
Gender : Inconnu
Phenotype : Cognitive impairment, Cognitive impairment, Cognitive impairment

Mean Coverage : 85 %

#47 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 254152
Gender : Inconnu

Mean Coverage : 85 %

#48 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 255967
Gender : Inconnu

Mean Coverage : 85 %

#49 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 257153
Gender : Inconnu

Mean Coverage : 85 %

#50 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 257155
Gender : Inconnu

Mean Coverage : 85 %

#51 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 258408
Gender : Inconnu

Mean Coverage : 85 %

#52 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 263127
Gender : Inconnu

Mean Coverage : 85 %

#53 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 267900
Gender : Inconnu

Mean Coverage : 85 %

#54 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 269994
Gender : Inconnu

Mean Coverage : 85 %

#55 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 272661
Gender : Inconnu
Phenotype : Intellectual disability

Mean Coverage : 85 %

#56 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 253296
Gender : Inconnu

Mean Coverage : 85 %

#57 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 253362
Gender : Inconnu

Mean Coverage : 85 %

#58 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 253363
Gender : Inconnu

Mean Coverage : 85 %

#59 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 253364
Gender : Inconnu

Mean Coverage : 85 %

#60 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 253365
Gender : Inconnu

Mean Coverage : 85 %

#61 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 325628
Gender : Inconnu
Phenotype : Intellectual disability, Obesity

Mean Coverage : 85 %

#62 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 326517
Gender : Inconnu
Phenotype : Specific learning disability, HP:0011398

Mean Coverage : 85 %

#63 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 331840
Gender : Inconnu
Phenotype : Intrauterine growth retardation, Intrauterine growth retardation

Mean Coverage : 85 %

#64 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 339285
Gender : Inconnu
Phenotype : Growth delay, Type I diabetes mellitus

Mean Coverage : 85 %

#65 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 339819
Gender : Inconnu
Phenotype : Global developmental delay, Obesity

Mean Coverage : 85 %

#66 : pathogenic
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 340588
Gender : Inconnu
Phenotype : Overgrowth, Intellectual disability, severe

Mean Coverage : 85 %

#67 : unknown
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

Patient Id : 341016
Gender : Inconnu

Mean Coverage : 85 %

#68 : pathogenic
Location : 28,708,185 - 29,088,624 | Size : 380,439 bases

Patient Id : 381680
Gender : Inconnu
Phenotype : Intrauterine growth retardation

Mean Coverage : 84 %

#69 : unknown
Location : 28,689,084 - 29,051,191 | Size : 362,107 bases

Patient Id : 283459
Gender : Inconnu
Phenotype : Autistic behavior, Autistic behavior, Autistic behavior

Mean Coverage : 83 %

#70 : pathogenic
Location : 28,689,084 - 29,051,191 | Size : 362,107 bases

Patient Id : 314116
Gender : Inconnu
Phenotype : Autism, Aggressive behavior, Generalized hypotonia, Severe global developmental delay

Mean Coverage : 83 %

#71 : unknown
Location : 28,689,084 - 29,043,863 | Size : 354,779 bases

Patient Id : 283458
Gender : Inconnu
Phenotype : Autistic behavior, Autistic behavior, Autistic behavior

Mean Coverage : 82 %

#72 : unknown
Location : 28,843,572 - 29,031,200 | Size : 187,628 bases

Patient Id : 278240
Gender : Inconnu
Phenotype : Intellectual disability, Intellectual disability

Mean Coverage : 81 %

#73 : pathogenic
Location : 28,843,753 - 29,031,071 | Size : 187,318 bases

Patient Id : 356980
Gender : Inconnu
Phenotype : Delayed speech and language development, Global developmental delay, Motor delay, Ischemic stroke, Left hemiplegia

Mean Coverage : 81 %

#74 : unknown
Location : 28,843,801 - 29,031,029 | Size : 187,228 bases

Patient Id : 255706
Gender : Inconnu

Mean Coverage : 81 %

#75 : unknown
Location : 28,843,801 - 29,031,029 | Size : 187,228 bases

Patient Id : 277613
Gender : Inconnu

Mean Coverage : 81 %

#76 : unknown
Location : 28,843,801 - 29,031,029 | Size : 187,228 bases

Patient Id : 280343
Gender : Inconnu

Mean Coverage : 81 %

#77 : unknown
Location : 28,843,801 - 29,031,029 | Size : 187,228 bases

Patient Id : 285452
Gender : Inconnu

Mean Coverage : 81 %

#78 : uncertain
Location : 28,843,801 - 29,031,029 | Size : 187,228 bases

Patient Id : 286534
Gender : Inconnu

Mean Coverage : 81 %

#79 : uncertain
Location : 28,843,801 - 29,031,029 | Size : 187,228 bases

Patient Id : 287625
Gender : Inconnu

Mean Coverage : 81 %

#80 : uncertain
Location : 28,843,801 - 29,031,029 | Size : 187,228 bases

Patient Id : 304096
Gender : Inconnu
Phenotype : Autism

Mean Coverage : 81 %

#81 : unknown
Location : 28,843,801 - 29,031,029 | Size : 187,228 bases

Patient Id : 314961
Gender : Inconnu

Mean Coverage : 81 %

#82 : unknown
Location : 28,843,802 - 29,031,030 | Size : 187,228 bases

Patient Id : 260398
Gender : Inconnu

Mean Coverage : 81 %

#83 : uncertain
Location : 28,843,802 - 29,031,030 | Size : 187,228 bases

Patient Id : 301347
Gender : Inconnu
Phenotype : Autistic behavior, Seizure, Abnormal fear\/anxiety\-related behavior, Autistic behavior, Seizure, Abnormal fear\/anxiety\-related behavior

Mean Coverage : 81 %

#84 : pathogenic
Location : 28,796,367 - 29,182,200 | Size : 385,833 bases

Patient Id : 305256
Gender : Inconnu

Mean Coverage : 80 %

#85 : unknown
Location : 28,861,559 - 29,031,029 | Size : 169,470 bases

Patient Id : 268487
Gender : Inconnu
Phenotype : Strabismus, Aggressive behavior, Intellectual disability, Truncal obesity, Strabismus, Aggressive behavior, Intellectual disability, Truncal obesity

Mean Coverage : 76 %

#86 : pathogenic
Location : 28,617,569 - 29,097,626 | Size : 480,057 bases

Patient Id : 270510
Gender : Inconnu
Phenotype : Shawl scrotum, Long face, Myoclonus, Plagiocephaly, Polyhydramnios, Ventriculomegaly, Generalized\-onset seizure, EEG abnormality, EEG with polyspike wave complexes, Focal myoclonic seizure, Severe global developmental delay, Shawl scrotum, Long face, Myoclonus, Plagiocephaly, Polyhydramnios, Ventriculomegaly, Generalized\-onset seizure, EEG abnormality, EEG with polyspike wave complexes, Focal myoclonic seizure, Severe global developmental delay

Mean Coverage : 73 %

0 Gene(s) in SFARI Database

0 DGV-Gold overlap(s) (>= 50% only)

0 DGV overlap(s) (>= 50% only)

5 Patient cases (>= 70% only)

28,833,294 - 29,037,247
Size : 203,953 bases
3 Reports

Mean Coverage : 85 %

28,833,435 - 29,008,513
Size : 175,078 bases
1 Reports

Mean Coverage : 78 %

28,833,435 - 29,046,284
Size : 212,849 bases
15 Reports

Mean Coverage : 87 %

28,833,494 - 29,037,108
Size : 203,614 bases
6 Reports

Mean Coverage : 85 %

28,833,494 - 29,037,107
Size : 203,613 bases
1 Reports

Mean Coverage : 85 %

1 Controls (>= 70% only)

nssv855478
Location : 28835494 - 29043450 | Size : 207956 bases

Mean Coverage : 86 %

6 Gene(s) in PanelApp Database

SH2B1 PanelApp Whole gene - Size : 27,612 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
Medium	Severe early-onset obesity	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	- obesity - Severe early-onset obesity-insulin resistance syndrome due to SH2B1 deficiency, MONDO:0017994	- Expert Review Amber - Expert list

ATP2A1 PanelApp Whole gene - Size : 26,061 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
High	Skeletal Muscle Channelopathies	BIALLELIC, autosomal or pseudoautosomal	- Brody myopathy 601003	- Expert Review Green - Expert list
Low	Other rare neuromuscular disorders	BIALLELIC, autosomal or pseudoautosomal	- Brody myopathy, 601003 - Brody Myopathy	- Expert Review Red
Low	Paroxysmal central nervous system disorders	BIALLELIC, autosomal or pseudoautosomal	- Brody myopathy, 601003	- Expert Review Red - NHS GMS - London North GLH - Wessex and West Midlands GLH
Low	Arthrogryposis	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	- Brody Myopathy - Brody myopathy, 601003	- Expert Review Red - Illumina TruGenome Clinical Sequencing Services - Emory Genetics Laboratory - Radboud University Medical Center, Nijmegen
Low	Congenital myopathy	BIALLELIC, autosomal or pseudoautosomal	- Brody myopathy, OMIM:601003	- Expert Review Red - Radboud University Medical Center, Nijmegen - Emory Genetics Laboratory - Illumina TruGenome Clinical Sequencing Services
High	Skeletal muscle channelopathy	BIALLELIC, autosomal or pseudoautosomal	- Brody myopathy OMIM:601003	- NHS GMS - Expert Review Green - London North GLH
Low	Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies	BIALLELIC, autosomal or pseudoautosomal	- Brody myopathy, 601003	- Expert Review Red - NHS GMS - Yorkshire and North East GLH - Expert Review
High	Severe Paediatric Disorders	BIALLELIC, autosomal or pseudoautosomal	- Brody myopathy, 601003	- Next Generation Children Project - Expert Review Green - Expert list
High	Severe Paediatric Disorders	BIALLELIC, autosomal or pseudoautosomal	- Brody myopathy, 601003	- Next Generation Children Project - Expert Review Green - Expert list

ATXN2L PanelApp Whole gene - Size : 14,238 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
Medium	Intellectual disability - microarray and sequencing	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	- Intellectual disability - Macrocephaly	- Expert Review Amber - Literature

CD19 PanelApp Whole gene - Size : 7,377 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
High	COVID-19 research	BIALLELIC, autosomal or pseudoautosomal	- Immunodeficiency, common variable, 3 - Isolated IgG subclass deficiency - Recurrent infections, may have glomerulonephritis - Immunodeficiency, common variable, 3 613493 - Common variable immunodeficiency disorders (CVID) - Predominantly Antibody Deficiencies - hypogammaglobulinemia	- IUIS Classification February 2018 - A- or hypo-gammaglobulinaemia v1.25 - London North GLH - NHS GMS - GRID V2.0 - Victorian Clinical Genetics Services - North West GLH - ESID Registry 20171117 - Expert Review Green - NHS GMS - North West GLH - London North GLH - IUIS Classification February 2018 - Victorian Clinical Genetics Services - Expert Review Green - ESID Registry 20171117 - GRID V2.0 - A- or hypo-gammaglobulinaemia v1.25
High	Primary immunodeficiency or monogenic inflammatory bowel disease	BIALLELIC, autosomal or pseudoautosomal	- Immunodeficiency, common variable, 3 613493 - hypogammaglobulinemia - Immunodeficiency, common variable, 3 - Common variable immunodeficiency disorders (CVID) - Isolated IgG subclass deficiency - Recurrent infections, may have glomerulonephritis - Predominantly Antibody Deficiencies	- NHS GMS - North West GLH - London North GLH - IUIS Classification February 2018 - Victorian Clinical Genetics Services - Expert Review Green - ESID Registry 20171117 - GRID V2.0 - A- or hypo-gammaglobulinaemia v1.25
High	Severe Paediatric Disorders	BIALLELIC, autosomal or pseudoautosomal	- Immunodeficiency, common variable, 3, 613493	- Next Generation Children Project - Expert Review Green - Expert list
High	Severe Paediatric Disorders	BIALLELIC, autosomal or pseudoautosomal	- Immunodeficiency, common variable, 3, 613493	- Next Generation Children Project - Expert Review Green - Expert list
High	Severe Paediatric Disorders	BIALLELIC, autosomal or pseudoautosomal	- Immunodeficiency, common variable, 3, 613493	- Next Generation Children Project - Expert Review Green - Expert list

LAT PanelApp Whole gene - Size : 5,958 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
High	COVID-19 research	BIALLELIC, autosomal or pseudoautosomal	- Immunodeficiencies affecting cellular and humoral immunity - Immunodeficiency 52, 617514 - Adenopathy, splenomegaly, recurrent infections, autoimmunity	- IUIS Classification February 2018 - SCID v1.6 - A- or hypo-gammaglobulinaemia v1.25 - London North GLH - NHS GMS - North West GLH - Combined B and T cell defect v1.12 - Expert Review Green - NHS GMS - North West GLH - London North GLH - Expert Review Green - IUIS Classification February 2018 - SCID v1.6 - Combined B and T cell defect v1.12 - A- or hypo-gammaglobulinaemia v1.25
Medium	Inherited bleeding disorders	BIALLELIC, autosomal or pseudoautosomal	- Immunodeficiency 52, 617514	- Expert Review Amber - Other
High	Primary immunodeficiency or monogenic inflammatory bowel disease	BIALLELIC, autosomal or pseudoautosomal	- Immunodeficiency 52, 617514 - Adenopathy, splenomegaly, recurrent infections, autoimmunity - Immunodeficiencies affecting cellular and humoral immunity	- Expert Review Green - Other - NHS GMS - North West GLH - London North GLH - IUIS Classification February 2018 - SCID v1.6 - Combined B and T cell defect v1.12 - A- or hypo-gammaglobulinaemia v1.25
Medium	Cytopenias and congenital anaemias	BIALLELIC, autosomal or pseudoautosomal	- Immunodeficiency 52, 617514	- Expert Review Amber - Other
Medium	Cytopenia - NOT Fanconi anaemia	BIALLELIC, autosomal or pseudoautosomal	- Immunodeficiency 52, 617514	- North West GLH - NHS GMS - Expert Review Amber - Wessex and West Midlands GLH
High	Severe Paediatric Disorders	BIALLELIC, autosomal or pseudoautosomal	- Immunodeficiency 52, 617514	- Next Generation Children Project - Expert Review Green - Expert list

TUFM PanelApp Whole gene - Size : 3,937 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
High	White matter disorders and cerebral calcification - narrow panel	BIALLELIC, autosomal or pseudoautosomal	- Mitochondrial Leukoencephalopathy - Combined oxidative phosphorylation deficiency 4, OMIM:610678	- Expert Review Green - NHS GMS
Medium	Inherited white matter disorders	BIALLELIC, autosomal or pseudoautosomal	- Mitochondrial Leukoencephalopathy	- Expert Review Amber - Expert list
High	Undiagnosed metabolic disorders	BIALLELIC, autosomal or pseudoautosomal	- Required for mitochondrial gene expression (Mitochondrial respiratory chain disorders (caused by nuclear variants only)) - Combined oxidative phosphorylation deficiency 4 610678	- Expert Review Green - Literature
High	Likely inborn error of metabolism - targeted testing not possible	BIALLELIC, autosomal or pseudoautosomal	- Required for mitochondrial gene expression (Mitochondrial respiratory chain disorders (caused by nuclear variants only)) - Multiple respiratory chain complex deficiencies (disorders of protein synthesis) - Combined oxidative phosphorylation deficiency 4 610678 - Combined oxidative phosphorylation deficiency 4, 610678	- Expert Review Green - Expert Review Green - London North GLH - NHS GMS - Victorian Clinical Genetics Services
High	Possible mitochondrial disorder - nuclear genes	BIALLELIC, autosomal or pseudoautosomal	- Combined oxidative phosphorylation deficiency 4, 610678	- Expert Review Green - NHS GMS
Medium	Fetal anomalies	BIALLELIC, autosomal or pseudoautosomal	- COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 4	- Expert Review Amber - PAGE DD-Gene2Phenotype
High	DDG2P	BIALLELIC, autosomal or pseudoautosomal	- COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 4 610678	- Expert Review Green - DD-Gene2Phenotype
Low	Intellectual disability - microarray and sequencing	BIALLELIC, autosomal or pseudoautosomal	- Combined oxidative phosphorylation deficiency 4, 610678	- Expert Review Red
High	Mitochondrial disorders	BIALLELIC, autosomal or pseudoautosomal	- Combined oxidative phosphorylation deficiency 4 610678	- Expert Review Green - Victorian Clinical Genetics Services - Radboud University Medical Center, Nijmegen - Expert list - Expert
Low	Childhood onset dystonia, chorea or related movement disorder			- Expert Review Red - London North GLH
High	Severe Paediatric Disorders	BIALLELIC, autosomal or pseudoautosomal	- Combined oxidative phosphorylation deficiency 4, 610678	- Next Generation Children Project - Expert Review Green - Expert list

ClassifyCNV ACMG Score

Pathogenic

ClassifyCNV ACMG Criteria

2A
+ 1

Complete overlap of an established HI gene/genomic region.

5B
-0.45

Patient with specific, well-defined phenotype and no family history. CNV is inherited from an apparently unaffected parent.

5D
+ 0.45

CNV segregates with a consistent phenotype observed in the patient’s family.

AnnotSV Score

Pathogenic

AnnotSV ACMG Criteria

2A
+ 1

Complete overlap of an established HI gene/genomic region.

5B
-0.45

Patient with specific, well-defined phenotype and no family history. CNV is inherited from an apparently unaffected parent.

5D
+ 0.45

CNV segregates with a consistent phenotype observed in the patient’s family.

Length (hg19) : 274,394 bases - Length (hg38) : 274,394 bases

CNV-Hub AChro-PucePIEV

AChro-Puce Criteria taken into account 1

2 Major

4 Major

4 Major

4 Major

4 Minor

4 Minor

4 Minor

ISV 2

XCNV 3

ClassifyCNV ACMG 4

AnnotSV ACMG 5

ACMG criteria

ClassifyCNV

2A + 1

5B -0.45

5D + 0.45

AnnotSV

2A + 1

5B -0.45

5D + 0.45

Diseases :

ClinGen

Decipher

DGV-Gold

0

0

DGV

0

0

Coe & Al study 6

5

1

Genes with pHaplo > 0.55 7

2

Genes with pTriplo > 0.68 7

4

Genes in SFARI

0

Genes in OMIM

9

Sources and references

9 OMIM Gene overlap(s)

Download genes as .csv

RABEP2 NM_024816.3 Whole gene - Size : 32,105 bases

Database :

SH2B1 NM_001387430.1 Whole gene - Size : 27,612 bases

Disease : Severe early-onset obesity-insulin resistance syndrome due to SH2B1 deficiency

Source : Orphanet

Database :

Human Phenotype Ontology Show/Hide

ATP2A1 NM_004320.6 Whole gene - Size : 26,061 bases

Disease : Brody myopathy

Source : Orphanet

Database :

Human Phenotype Ontology Show/Hide

NFATC2IP NM_032815.4 Whole gene - Size : 16,285 bases

Database :

ATXN2L NM_007245.4 Whole gene - Size : 14,238 bases

Database :

SPNS1 NM_032038.3 Whole gene - Size : 10,327 bases

Database :

CD19 NM_001770.6 Whole gene - Size : 7,377 bases

Disease : Common variable immunodeficiency

Source : Orphanet

Database :

Human Phenotype Ontology Show/Hide

LAT NM_001014987.2 Whole gene - Size : 5,958 bases

Disease : Severe combined immunodeficiency due to LAT deficiency

Source : Orphanet

Database :

Human Phenotype Ontology Show/Hide

TUFM NM_003321.5 Whole gene - Size : 3,937 bases

Disease : Combined oxidative phosphorylation defect type 4

Source : Orphanet

Database :

Human Phenotype Ontology Show/Hide

17 Non-OMIM Gene overlap(s)

CNV-Hub AChro-Puce
PIEV

AChro-Puce Criteria taken into account¹

ISV²

XCNV³

ClassifyCNV ACMG⁴

AnnotSV ACMG⁵

2A
+ 1

5B
-0.45

5D
+ 0.45

2A
+ 1

5B
-0.45

5D
+ 0.45

Coe & Al study⁶

Genes with pHaplo > 0.55⁷

Genes with pTriplo > 0.68⁷

ENSG00000261067
Size : 15,971 bases

ENSG00000251417
Size : 15,085 bases

NFATC2IP-AS1
Size : 14,067 bases

NPIPB10P
Size : 14,071 bases

ENSG00000260570
Size : 6,588 bases

ENSG00000260367
Size : 4,862 bases

ENSG00000278528
Size : 3,710 bases

ENSG00000240634
Size : 693 bases

ENSG00000260796
Size : 1,463 bases

ENSG00000275807
Size : 1,538 bases

ENSG00000261766
Size : 1,174 bases

ATP2A1-AS1
Size : 2,000 bases

ENSG00000261552
Size : 1,638 bases

NOVEL
Size : 103 bases

KNOWN
Size : 88 bases

NOVEL
Size : 127 bases

KNOWN
Size : 78 bases

#1 Pathogenic (16p11.2)
Location : 28,802,396 - 29,051,191 | Size : 248,795 bases

#2 Pathogenic (16p11.2)
Location : 28,763,833 - 29,051,191 | Size : 287,358 bases

#3 Pathogenic (16p11.2)
Location : 28,763,834 - 29,051,191 | Size : 287,357 bases

#4 Pathogenic (nssv13644823)
Location : 28,763,833 - 29,043,863 | Size : 280,030 bases

#5 Pathogenic (16p11.2)
Location : 28,747,519 - 29,051,191 | Size : 303,672 bases

#6 Pathogenic (16p11.2)
Location : 28,819,027 - 29,051,191 | Size : 232,164 bases

#7 Pathogenic (nssv3397222)
Location : 28,819,027 - 29,051,191 | Size : 232,164 bases

#8 Pathogenic (nssv13652140)
Location : 28,819,027 - 29,043,972 | Size : 224,945 bases

#9 Pathogenic (nssv1609384)
Location : 28,820,742 - 29,044,776 | Size : 224,034 bases

#10 Pathogenic (nssv1610312)
Location : 28,824,793 - 29,044,776 | Size : 219,983 bases

#11 Pathogenic (nssv1604382)
Location : 28,824,793 - 29,043,960 | Size : 219,167 bases

#12 Pathogenic (16p11.2)
Location : 28,825,604 - 29,043,450 | Size : 217,846 bases

#13 Pathogenic (16p11.2)
Location : 28,826,161 - 29,043,960 | Size : 217,799 bases

#14 Pathogenic (nssv1609601)
Location : 28,733,738 - 29,044,776 | Size : 311,038 bases

#15 Pathogenic (16p11.2)
Location : 28,734,570 - 29,043,450 | Size : 308,880 bases

#16 Pathogenic/Likely pathogenic (nssv13642995)
Location : 28,826,161 - 29,043,901 | Size : 217,740 bases

#17 Pathogenic (nssv3396771)
Location : 28,708,172 - 29,051,191 | Size : 343,019 bases

#18 Pathogenic (nssv577891)
Location : 28,721,798 - 29,037,107 | Size : 315,309 bases

#19 Pathogenic (Single allele)
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

#20 Pathogenic (nssv578114)
Location : 28,837,449 - 29,042,118 | Size : 204,669 bases

#21 Pathogenic (16p11.2)
Location : 28,837,904 - 29,088,624 | Size : 250,720 bases

#22 Pathogenic (16p11.2)
Location : 28,689,084 - 29,051,191 | Size : 362,107 bases

#23 Pathogenic (16p11.2)
Location : 28,689,084 - 29,051,191 | Size : 362,107 bases

#24 Pathogenic (nssv1610483)
Location : 28,689,084 - 29,051,191 | Size : 362,107 bases

#25 Likely pathogenic (nssv1415448)
Location : 28,824,793 - 29,133,735 | Size : 308,942 bases

#26 Pathogenic (nssv1603731)
Location : 28,843,753 - 29,031,071 | Size : 187,318 bases

#27 Pathogenic (nssv578225)
Location : 28,854,628 - 29,037,107 | Size : 182,479 bases

#28 Pathogenic (nssv1415380)
Location : 28,861,530 - 29,043,960 | Size : 182,430 bases

#29 Pathogenic (16p11.2)
Location : 28,784,626 - 29,230,353 | Size : 445,727 bases

#30 Pathogenic (16p11.2)
Location : 28,819,027 - 28,988,225 | Size : 169,198 bases

#31 Pathogenic (16p11.2)
Location : 28,861,530 - 29,031,059 | Size : 169,529 bases

#32 Pathogenic (nssv707120)
Location : 28,861,530 - 29,031,059 | Size : 169,529 bases

#33 Likely pathogenic (Single allele)
Location : 28,668,058 - 29,001,338 | Size : 333,280 bases

#34 Pathogenic (g.)
Location : 28,854,295 - 29,001,333 | Size : 147,038 bases

#1 : pathogenic
Location : 28,796,367 - 29,076,269 | Size : 279,902 bases

#2 : pathogenic
Location : 28,796,367 - 29,076,269 | Size : 279,902 bases

#3 : pathogenic
Location : 28,748,615 - 29,051,191 | Size : 302,576 bases

#4 : unknown
Location : 28,819,027 - 29,051,191 | Size : 232,164 bases

#5 : pathogenic
Location : 28,824,856 - 29,051,191 | Size : 226,335 bases

#6 : unknown
Location : 28,823,914 - 29,043,863 | Size : 219,949 bases

#7 : unknown
Location : 28,824,793 - 29,044,776 | Size : 219,983 bases

#8 : unknown
Location : 28,824,793 - 29,044,776 | Size : 219,983 bases

#9 : unknown
Location : 28,824,793 - 29,044,776 | Size : 219,983 bases

#10 : unknown
Location : 28,824,793 - 29,044,716 | Size : 219,923 bases

#11 : uncertain
Location : 28,824,777 - 29,039,612 | Size : 214,835 bases

#12 : uncertain
Location : 28,824,777 - 29,039,612 | Size : 214,835 bases

#13 : uncertain
Location : 28,824,777 - 29,039,612 | Size : 214,835 bases

#14 : uncertain
Location : 28,824,777 - 29,039,612 | Size : 214,835 bases