hg19 LOSS chr10-46100000-49900000

Length (hg19) : 3,800,000 bases - Length (hg38) : 3,087,403 bases

CNV-Hub AChro-Puce
Uncertain

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

2 Major

At least 1 occurrence in DGV / DGV-Gold > 80 % overlaps

Class

2 Minor

At least 1 occurrence in DGV / DGV-Gold > 50 % overlaps

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 Minor

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

Class

4 Minor

CNV length of 1 Mb or more

ISV²

XCNV³

ClassifyCNV ACMG⁴

AnnotSV ACMG⁵

ACMG criteria

ClassifyCNV

2H
+ 0.15

Multiple HI predictors suggest that AT LEAST ONE gene in the interval is haploinsufficient (HI).

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.

3C
+ 0.9

Number of protein-coding RefSeq genes wholly or partially included in the CNV 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.

ClinGen

0 benign CNV
0 likely benign CNV
1 uncertain CNV
3 likely pathogenic CNV
12 pathogenic CNV

70% Overlaps

Decipher

0 benign CNV
5 unknown CNV
4 uncertain CNV
4 pathogenic CNV

70% Overlaps

DGV-Gold

0

80% Overlaps

0

50% Overlaps

DGV

1

80% Overlaps

1

50% Overlaps

Coe & Al study⁶

1

Patient cases
70% Overlaps

1

Controls
70% Overlaps

Genes with pHaplo > 0.55⁷

2

MAPK8 WDFY4

Genes with pTriplo > 0.68⁷

1

MAPK8

Genes in SFARI

1

WDFY4

Genes in OMIM

12 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

12 OMIM Gene overlap(s)

Download genes as .csv

WDFY4 NM_001394531.1 Exons 1->1 / 62 - Size : 298,083 bases

pLI : 0.34 LOEUF : 0.3 pHaplo : 0.79 pTriplo : 0.26
Location : 49,892,918 - 50,191,001

Database :

DecipherGenomics OMIM:613316 GTEx Portal Human Protein Atlas Ensembl

SFARI (Autism Database) :

Gene Score : 2

Is Not Syndromic

No EAGLE Score

Reports : 8

ARHGAP22 NM_021226.4 Exons 1->10 / 10 - Size : 210,231 bases

pLI : 0 LOEUF : 0.93 sHet : 0.026 pHaplo : 0.18 pTriplo : 0.59
Location : 49,654,079 - 49,864,310

Database :

DecipherGenomics OMIM:610585 GTEx Portal Human Protein Atlas Ensembl

MAPK8 NM_001323329.2 Exons 1->12 / 12 - Size : 132,721 bases

pLI : 1 LOEUF : 0.21 sHet : 0.081 pHaplo : 0.61 pTriplo : 0.97
Location : 49,514,682 - 49,647,403

Database :

DecipherGenomics PanelApp OMIM:601158 GTEx Portal Human Protein Atlas Ensembl

Human Phenotype Ontology Show/Hide

HP:0031819	Increased waist to hip ratio	Increased waist-to-hip ratio (WHR) is a measurement above the average for the dimensionless ratio of the circumference of the waist to that of the hips. WHR is calculated as waist measurement divided by hip measurement.
HP:0005978	Type II diabetes mellitus	A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia.
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:0003584	Late onset	A type of adult onset with onset of symptoms after the age of 60 years.
HP:0000855	Insulin resistance	Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels.

FRMPD2 NM_001018071.4 Exons 1->29 / 29 - Size : 121,608 bases

pLI : 0 LOEUF : 1.18 sHet : 0.004 pHaplo : 0.08 pTriplo : 0.27
Location : 49,361,131 - 49,482,739

Database :

DecipherGenomics OMIM:613323 GTEx Portal Human Protein Atlas Ensembl

WASHC2C NM_001330074.2 Whole gene - Size : 65,764 bases

pLI : 0 LOEUF : 0.86
Location : 46,222,648 - 46,288,412

Database :

DecipherGenomics OMIM:613631 GTEx Portal Human Protein Atlas Ensembl

ANXA8 NM_001040084.3 Whole gene - Size : 23,996 bases

pHaplo : 0.18 pTriplo : 0.58
Location : 48,255,204 - 48,279,200

Database :

DecipherGenomics OMIM:602396 GTEx Portal Human Protein Atlas Ensembl

SYT15 NM_031912.5 Whole gene - Size : 15,956 bases

pLI : 0 LOEUF : 1.78 pHaplo : 0.11 pTriplo : 0.3
Location : 46,955,444 - 46,971,400

Database :

DecipherGenomics PanelApp OMIM:608081 GTEx Portal Human Protein Atlas Ensembl

GPRIN2 NM_001385282.1 Whole gene - Size : 14,922 bases

pLI : 0 LOEUF : 1.49 sHet : 0.004 pHaplo : 0.12 pTriplo : 0.29
Location : 46,992,959 - 47,007,881

Database :

DecipherGenomics OMIM:611240 GTEx Portal Human Protein Atlas Ensembl

GDF10 NM_004962.5 Whole gene - Size : 13,380 bases

sHet : 0.043 pHaplo : 0.52 pTriplo : 0.57
Location : 48,425,785 - 48,439,165

Database :

DecipherGenomics OMIM:601361 GTEx Portal Human Protein Atlas Ensembl

RBP3 NM_002900.3 Whole gene - Size : 9,518 bases

sHet : 0.027 pHaplo : 0.18 pTriplo : 0.22
Location : 48,381,481 - 48,390,999

Database :

DecipherGenomics PanelApp OMIM:180290 GTEx Portal Human Protein Atlas Ensembl

Human Phenotype Ontology Show/Hide

HP:0000501	Glaucoma	Glaucoma refers loss of retinal ganglion cells in a characteristic pattern of optic neuropathy usually associated with increased intraocular pressure.
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:0001419	X-linked recessive inheritance	A mode of inheritance that is observed for recessive traits related to a gene encoded on the X chromosome. In the context of medical genetics, X-linked recessive disorders manifest in males (who have one copy of the X chromosome and are thus hemizygotes), but generally not in female heterozygotes who have one mutant and one normal allele.
HP:0007663	Reduced visual acuity
HP:0005978	Type II diabetes mellitus	A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia.
HP:0000842	Hyperinsulinemia	An increased concentration of insulin in the blood.
HP:0008046	Abnormal retinal vascular morphology	A structural abnormality of retinal vasculature.
HP:0003581	Adult onset	Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later.
HP:0000543	Optic disc pallor	A pale yellow discoloration of the optic disk (the area of the optic nerve head in the retina). The optic disc normally has a pinkish hue with a central yellowish depression.
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:0000431	Wide nasal bridge	Increased breadth of the nasal bridge (and with it, the nasal root).
HP:0007675	Progressive night blindness
HP:0001133	Constriction of peripheral visual field	An absolute or relative decrease in retinal sensitivity extending from edge (periphery) of the visual field in a concentric pattern. The visual field is the area that is perceived simultaneously by a fixating eye.
HP:0031605	Abnormality of fundus pigmentation	Any anomaly of the pigmentation of the fundus, the posterior part of the eye including the retina and optic nerve.
HP:0000987	Atypical scarring of skin	Atypically scarred skin .
HP:0000613	Photophobia	Excessive sensitivity to light with the sensation of discomfort or pain in the eyes due to exposure to bright light.
HP:0000648	Optic atrophy	Atrophy of the optic nerve. Optic atrophy results from the death of the retinal ganglion cell axons that comprise the optic nerve and manifesting as a pale optic nerve on fundoscopy.
HP:0007703	Abnormality of retinal pigmentation
HP:0000563	Keratoconus	A cone-shaped deformity of the cornea characterized by the presence of corneal distortion secondary to thinning of the apex.
HP:0000463	Anteverted nares	Anteriorly-facing nostrils viewed with the head in the Frankfurt horizontal and the eyes of the observer level with the eyes of the subject. This gives the appearance of an upturned nose (upturned nasal tip).
HP:0000505	Visual impairment	Visual impairment (or vision impairment) is vision loss (of a person) to such a degree as to qualify as an additional support need through a significant limitation of visual capability resulting from either disease, trauma, or congenital or degenerative conditions that cannot be corrected by conventional means, such as refractive correction, medication, or surgery.
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:0000639	Nystagmus	Rhythmic, involuntary oscillations of one or both eyes related to abnormality in fixation, conjugate gaze, or vestibular mechanisms.
HP:0000518	Cataract	A cataract is an opacity or clouding that develops in the crystalline lens of the eye or in its capsule.
HP:0000602	Ophthalmoplegia	Paralysis of one or more extraocular muscles that are responsible for eye movements.
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:0000662	Nyctalopia	Inability to see well at night or in poor light.
HP:0007737	Bone spicule pigmentation of the retina	Pigment migration into the retina in a bone-spicule configuration (resembling the nucleated cells within the lacuna of bone).
HP:0000035	Abnormal testis morphology	An anomaly of the testicle (the male gonad).
HP:0000603	Central scotoma	An area of depressed vision located at the point of fixation and that interferes with central vision.
HP:0000618	Blindness	Blindness is the condition of lacking visual perception defined as visual perception below 3/60 and/or a visual field of no greater than 10 degrees in radius around central fixation.
HP:0008736	Hypoplasia of penis
HP:0001513	Obesity	Accumulation of substantial excess body fat.
HP:0000135	Hypogonadism	A decreased functionality of the gonad.
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:0001347	Hyperreflexia	Hyperreflexia is the presence of hyperactive stretch reflexes of the muscles.
HP:0000512	Abnormal electroretinogram	Any abnormality of the electrical responses of various cell types in the retina as measured by electroretinography.
HP:0007787	Posterior subcapsular cataract	A type of cataract affecting the posterior pole of lens immediately adjacent to ('beneath') the Lens capsule.

GDF2 NM_016204.4 Whole gene - Size : 5,134 bases

sHet : 0.009 pHaplo : 0.16 pTriplo : 0.23
Location : 48,411,774 - 48,416,908

Database :

DecipherGenomics PanelApp OMIM:605120 GTEx Portal Human Protein Atlas Ensembl

Human Phenotype Ontology Show/Hide

HP:0002092	Pulmonary arterial hypertension	Pulmonary hypertension is defined mean pulmonary artery pressure of 25mmHg or more and pulmonary capillary wedge pressure of 15mmHg or less when measured by right heart catheterisation at rest and in a supine position.
HP:0100659	Abnormal cerebral vascular morphology	An anomaly of the cerebral blood vessels.
HP:0001409	Portal hypertension	Increased pressure in the portal vein.
HP:0002040	Esophageal varix	Extreme dilation of the submucusoal veins in the lower portion of the esophagus.
HP:0011025	Abnormal cardiovascular system physiology	Abnormal functionality of the cardiovascular system.
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:0000787	Nephrolithiasis	The presence of calculi (stones) in the kidneys.
HP:0000421	Epistaxis	Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose.
HP:0007420	Spontaneous hematomas	Spontaneous development of hematomas (hematoma) or bruises without significant trauma.
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:0001082	Cholecystitis	The presence of inflammatory changes in the gallbladder.
HP:0001342	Cerebral hemorrhage	Hemorrhage into the parenchyma of the brain.
HP:0001009	Telangiectasia	Telangiectasias refer to small dilated blood vessels located near the surface of the skin or mucous membranes, measuring between 0.5 and 1 millimeter in diameter. Telangiectasia are located especially on the tongue, lips, palate, fingers, face, conjunctiva, trunk, nail beds, and fingertips.
HP:0000524	Conjunctival telangiectasia	The presence of small (ca. 0.5-1.0 mm) dilated blood vessels near the surface of the mucous membranes of the conjunctiva.
HP:0002138	Subarachnoid hemorrhage	Hemorrhage occurring between the arachnoid mater and the pia mater.
HP:0100585	Telangiectasia of the skin	Presence of small, permanently dilated blood vessels near the surface of the skin, visible as small focal red lesions.
HP:0100761	Visceral angiomatosis
HP:0001394	Cirrhosis	A chronic disorder of the liver in which liver tissue becomes scarred and is partially replaced by regenerative nodules and fibrotic tissue resulting in loss of liver function.
HP:0001635	Congestive heart failure	The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction.
HP:0002105	Hemoptysis	Coughing up (expectoration) of blood or blood-streaked sputum from the larynx, trachea, bronchi, or lungs.
HP:0000646	Amblyopia	Reduced visual acuity that is uncorrectable by lenses in the absence of detectable anatomic defects in the eye or visual pathways.
HP:0000790	Hematuria	The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine).
HP:0001048	Cavernous hemangioma	The presence of a cavernous hemangioma. A hemangioma characterized by large endothelial spaces (caverns) is called a cavernous hemangioma.
HP:0100784	Peripheral arteriovenous fistula
HP:0002204	Pulmonary embolism	An embolus (that is, an abnormal particle circulating in the blood) located in the pulmonary artery and thereby blocking blood circulation to the lung. Usually the embolus is a blood clot that has developed in an extremity (for instance, a deep venous thrombosis), detached, and traveled through the circulation before becoming trapped in the pulmonary artery.
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:0001399	Hepatic failure
HP:0004936	Venous thrombosis	Formation of a blood clot (thrombus) inside a vein, causing the obstruction of blood flow.
HP:0100026	Arteriovenous malformation	An anomalous configuration of blood vessels that shunts arterial blood directly into veins without passing through the capillaries.
HP:0001935	Microcytic anemia	A kind of anemia in which the volume of the red blood cells is reduced.
HP:0002326	Transient ischemic attack
HP:0200008	Intestinal polyposis	The presence of multiple polyps in the intestine.
HP:0004406	Spontaneous, recurrent epistaxis
HP:0002239	Gastrointestinal hemorrhage	Hemorrhage affecting the gastrointestinal tract.
HP:0002076	Migraine	Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms.
HP:0001081	Cholelithiasis	Hard, pebble-like deposits that form within the gallbladder.
HP:0007763	Retinal telangiectasia	Dilatation of small blood vessels of the retina.
HP:0100579	Mucosal telangiectasiae	Telangiectasia of the mucosa, the mucous membranes which are involved in absorption and secretion that line cavities that are exposed to the external environment and internal organs.

NPY4R NM_005972.6 Whole gene - Size : 4,863 bases

pLI : 0 LOEUF : 1.75 sHet : 0.004 pHaplo : 0.14 pTriplo : 0.25
Location : 47,083,457 - 47,088,320

Database :

DecipherGenomics OMIM:601790 GTEx Portal Human Protein Atlas Ensembl

104 Non-OMIM Gene overlap(s)

NOVEL
Size : 162,265 bases

Location : 47,011,753 - 47,174,018

ENSG00000289143
Size : 130,349 bases

Location : 49,218,162 - 49,348,511

KNOWN
Size : 91,090 bases

Location : 46,549,955 - 46,641,045

KNOWN
Size : 91,092 bases

Location : 48,736,874 - 48,827,966

ENSG00000289444
Size : 103,796 bases

Location : 49,244,696 - 49,348,492

ZFAND4
Size : 57,280 bases

pLI : 0 LOEUF : 1.06 pHaplo : 0.09 pTriplo : 0.25
Location : 46,110,948 - 46,168,228

KNOWN
Size : 62,078 bases

Location : 46,349,541 - 46,411,619

KNOWN
Size : 55,389 bases

Location : 47,894,023 - 47,949,412

KNOWN
Size : 53,415 bases

Location : 48,001,603 - 48,055,018

KNOWN
Size : 49,870 bases

Location : 48,901,102 - 48,950,972

PTPN20CP
Size : 55,150 bases

Location : 49,272,348 - 49,327,498

KNOWN
Size : 47,894 bases

Location : 47,191,844 - 47,239,738

NOVEL
Size : 35,697 bases

Location : 47,207,805 - 47,243,502

KNOWN
Size : 40,985 bases

Location : 47,379,727 - 47,420,712

ANTXRLP1
Size : 39,672 bases

Location : 47,605,121 - 47,644,793

ANTXRL
Size : 43,862 bases

pHaplo : 0.25 pTriplo : 0.32
Location : 47,657,581 - 47,701,443

FAM245B
Size : 30,723 bases

Location : 48,119,958 - 48,150,681

KNOWN
Size : 47,896 bases

Location : 48,189,612 - 48,237,508

LINC02675
Size : 30,813 bases

Location : 48,987,624 - 49,018,437

ENSG00000290899
Size : 34,945 bases

Location : 49,313,240 - 49,348,185

AGAP10P
Size : 21,840 bases

Location : 46,174,140 - 46,195,980

FAM21FP
Size : 16,008 bases

Location : 46,201,879 - 46,217,887

AGAP4
Size : 28,281 bases

pHaplo : 0.14 pTriplo : 0.24
Location : 46,321,042 - 46,349,323

KNOWN
Size : 24,468 bases

Location : 46,657,135 - 46,681,603

KNOWN
Size : 15,946 bases

Location : 46,717,127 - 46,733,073

KNOWN
Size : 23,593 bases

Location : 46,737,612 - 46,761,205

SHLD2P1
Size : 20,974 bases

Location : 46,918,169 - 46,939,143

ENSG00000229227
Size : 14,236 bases

Location : 46,937,463 - 46,951,699

SYT15-AS1
Size : 17,442 bases

Location : 46,951,467 - 46,968,909

SYT15B
Size : 18,889 bases

Location : 46,952,511 - 46,971,400

KNOWN
Size : 16,110 bases

Location : 47,157,983 - 47,174,093

KNOWN
Size : 13,576 bases

Location : 47,228,366 - 47,241,942

NOVEL
Size : 10,760 bases

Location : 47,279,073 - 47,289,833

AGAP14P
Size : 21,480 bases

Location : 47,708,453 - 47,729,933

ENSG00000279458
Size : 11,909 bases

Location : 47,741,976 - 47,753,885

KNOWN
Size : 16,105 bases

Location : 47,746,936 - 47,763,041

NOVEL
Size : 23,909 bases

Location : 47,746,962 - 47,770,871

KNOWN
Size : 11,840 bases

Location : 48,187,416 - 48,199,256

KNOWN
Size : 12,880 bases

Location : 48,249,334 - 48,262,214

NOVEL
Size : 23,920 bases

Location : 48,255,279 - 48,279,199

ZNF488
Size : 18,797 bases

sHet : 0.009 pHaplo : 0.21 pTriplo : 0.45
Location : 48,355,069 - 48,373,866

ENSG00000289299
Size : 17,549 bases

Location : 48,514,368 - 48,531,917

KNOWN
Size : 24,468 bases

Location : 48,844,036 - 48,868,504

KNOWN
Size : 27,778 bases

Location : 48,952,491 - 48,980,269

AGAP12P
Size : 21,719 bases

Location : 49,217,898 - 49,239,617

AGAP12P
Size : 21,501 bases

Location : 49,218,157 - 49,239,658

BMS1P7
Size : 9,756 bases

Location : 49,258,304 - 49,268,060

ENSG00000290460
Size : 9,205 bases

Location : 46,213,474 - 46,222,679

ENSG00000228702
Size : 344 bases

Location : 46,221,142 - 46,221,486

ENSG00000270434
Size : 296 bases

Location : 46,308,096 - 46,308,392

FAM25E
Size : 1,896 bases

pHaplo : 0.09 pTriplo : 0.35
Location : 46,310,876 - 46,312,772

FAM25E
Size : 1,763 bases

pHaplo : 0.09 pTriplo : 0.35
Location : 46,310,934 - 46,312,697

RNA5SP310
Size : 115 bases

Location : 46,351,755 - 46,351,870

KNOWN
Size : 115 bases

Location : 46,742,028 - 46,742,143

KNOWN
Size : 6,100 bases

Location : 46,772,794 - 46,778,894

KNOWN
Size : 1,759 bases

Location : 46,773,447 - 46,775,206

KNOWN
Size : 1,118 bases

Location : 46,790,404 - 46,791,522

KNOWN
Size : 283 bases

Location : 46,900,386 - 46,900,669

LINC02637
Size : 3,085 bases

Location : 46,914,145 - 46,917,230

RHEBP1
Size : 555 bases

Location : 46,914,151 - 46,914,706

ENSG00000290913
Size : 9,216 bases

Location : 46,914,472 - 46,923,688

NPY4R2
Size : 4,863 bases

Location : 47,083,457 - 47,088,320

HNRNPA1P33
Size : 560 bases

Location : 47,133,338 - 47,133,898

ENSG00000273760
Size : 3,451 bases

Location : 47,135,135 - 47,138,586

KNOWN
Size : 297 bases

Location : 47,174,442 - 47,174,739

KNOWN
Size : 4,477 bases

Location : 47,177,204 - 47,181,681

NOVEL
Size : 5,982 bases

Location : 47,186,203 - 47,192,185

KNOWN
Size : 115 bases

Location : 47,222,341 - 47,222,456

KNOWN
Size : 1,760 bases

Location : 47,254,247 - 47,256,007

KNOWN
Size : 1,120 bases

Location : 47,271,222 - 47,272,342

KNOWN
Size : 283 bases

Location : 47,382,464 - 47,382,747

KNOWN
Size : 599 bases

Location : 47,396,223 - 47,396,822

KNOWN
Size : 3,359 bases

Location : 47,570,513 - 47,573,872

KNOWN
Size : 1,272 bases

Location : 47,594,379 - 47,595,651

KNOWN
Size : 1,149 bases

Location : 47,656,084 - 47,657,233

FAM25BP
Size : 4,437 bases

Location : 47,740,330 - 47,744,767

ENSG00000290780
Size : 3,260 bases

Location : 47,741,564 - 47,744,824

KNOWN
Size : 1,563 bases

Location : 47,965,760 - 47,967,323

CTSLP2
Size : 6,142 bases

Location : 48,152,549 - 48,158,691

KNOWN
Size : 1,107 bases

Location : 48,157,041 - 48,158,148

KNOWN
Size : 6,145 bases

Location : 48,169,665 - 48,175,810

KNOWN
Size : 1,759 bases

Location : 48,173,347 - 48,175,106

KNOWN
Size : 115 bases

Location : 48,206,895 - 48,207,010

KNOWN
Size : 4,474 bases

Location : 48,247,669 - 48,252,143

KNOWN
Size : 299 bases

Location : 48,254,606 - 48,254,905

KNOWN
Size : 7,409 bases

Location : 48,324,788 - 48,332,197

KNOWN
Size : 674 bases

Location : 48,357,926 - 48,358,600

NOVEL
Size : 98 bases

Location : 48,387,524 - 48,387,622

KNOWN
Size : 115 bases

Location : 48,931,789 - 48,931,904

ENSG00000265630
Size : 6,096 bases

Location : 48,962,529 - 48,968,625

KNOWN
Size : 946 bases

Location : 48,963,181 - 48,964,127

KNOWN
Size : 1,111 bases

Location : 48,980,162 - 48,981,273

KNOWN
Size : 7,117 bases

Location : 49,087,398 - 49,094,515

KNOWN
Size : 283 bases

Location : 49,090,136 - 49,090,419

FAM25C
Size : 4,470 bases

pHaplo : 0.09 pTriplo : 0.39
Location : 49,203,355 - 49,207,825

RNA5SP315
Size : 115 bases

Location : 49,248,476 - 49,248,591

NOVEL
Size : 809 bases

Location : 49,363,368 - 49,364,177

ENSG00000285786
Size : 1,987 bases

Location : 49,454,568 - 49,456,555

RPS6P14
Size : 718 bases

Location : 49,500,742 - 49,501,460

ENSG00000279822
Size : 1,984 bases

Location : 49,651,879 - 49,653,863

ARHGAP22-IT1
Size : 1,064 bases

Location : 49,718,568 - 49,719,632

ENSG00000231906
Size : 241 bases

Location : 49,754,517 - 49,754,758

ENSG00000251413
Size : 1,089 bases

Location : 49,832,049 - 49,833,138

ENSG00000236800
Size : 8,225 bases

Location : 49,872,244 - 49,880,469

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

0 Benign CNV 0 Likely benign CNV 1 Uncertain CNV 3 Likely pathogenic CNV 12 Pathogenic CNV

#1 Pathogenic (nssv583185)
Location : 46,205,689 - 51,330,432 | Size : 5,124,743 bases

Score : 0

Mean Coverage : 83 %

#2 Pathogenic (10q11.22-11.23)
Location : 46,491,168 - 51,081,560 | Size : 4,590,392 bases

Score : 1

Mean Coverage : 81 %

#3 Pathogenic (nssv13646749)
Location : 46,224,445 - 51,594,991 | Size : 5,370,546 bases

Score : 0

Mean Coverage : 80 %

#4 Pathogenic (nssv706778)
Location : 46,205,695 - 51,724,915 | Size : 5,519,220 bases

Score : 0

Mean Coverage : 79 %

#5 Pathogenic (10q11.22-11.23)
Location : 46,287,820 - 51,627,470 | Size : 5,339,650 bases

Score : 0

Mean Coverage : 79 %

#6 not provided (10q11.22-11.23)
Location : 46,321,317 - 51,595,050 | Size : 5,273,733 bases

Score : 0

Mean Coverage : 79 %

#7 Pathogenic (nssv579668)
Location : 46,205,689 - 51,911,085 | Size : 5,705,396 bases

Score : 1

Mean Coverage : 78 %

#8 Pathogenic (10q11.22-11.23)
Location : 46,225,363 - 51,874,356 | Size : 5,648,993 bases

Score : 0

Mean Coverage : 78 %

#9 Pathogenic (10q11.22-11.23)
Location : 46,235,356 - 51,874,163 | Size : 5,638,807 bases

Score : 0

Mean Coverage : 78 %

#10 Likely pathogenic (10q11.22-11.23)
Location : 46,269,492 - 51,874,356 | Size : 5,604,864 bases

Score : 1

Mean Coverage : 77 %

#11 Pathogenic (10q11.22-11.23)
Location : 46,287,820 - 51,861,565 | Size : 5,573,745 bases

Score : 0

Mean Coverage : 77 %

#12 Pathogenic (nssv583520)
Location : 46,491,168 - 51,594,991 | Size : 5,103,823 bases

Score : 0

Mean Coverage : 77 %

#13 Uncertain significance (nssv1610028)
Location : 46,476,964 - 51,724,915 | Size : 5,247,951 bases

Score : 0

Mean Coverage : 76 %

#14 Likely pathogenic (nssv1495736)
Location : 46,476,964 - 51,724,915 | Size : 5,247,951 bases

Score : 0

Mean Coverage : 76 %

#15 Likely pathogenic (nssv1602988)
Location : 46,491,168 - 51,664,079 | Size : 5,172,911 bases

Score : 0

Mean Coverage : 76 %

#16 Pathogenic (10q11.22-11.23)
Location : 46,544,809 - 51,743,471 | Size : 5,198,662 bases

Score : 1

Mean Coverage : 75 %

#17 Pathogenic (10q11.22-11.23)
Location : 46,576,514 - 51,680,164 | Size : 5,103,650 bases

Score : 0
Phenotype : Telangiectasia,hereditary hemorrhagic,type 5

Mean Coverage : 75 %

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

0 Benign CNV 5 Unknown CNV 4 Uncertain CNV 4 Pathogenic CNV

#1 : unknown
Location : 46,248,489 - 51,572,974 | Size : 5,324,485 bases

Patient Id : 254072
Gender : Inconnu
Phenotype : Glossoptosis, Cleft palate, Epicanthus, Hypertelorism, Micrognathia

Mean Coverage : 80 %

#2 : uncertain
Location : 46,205,719 - 51,911,060 | Size : 5,705,341 bases

Patient Id : 339993
Gender : Inconnu
Phenotype : Strabismus, Seizure, Mild global developmental delay

Mean Coverage : 78 %

#3 : pathogenic
Location : 46,241,892 - 51,829,561 | Size : 5,587,669 bases

Patient Id : 295571
Gender : Inconnu
Phenotype : Otitis media, Joint hypermobility, Short stature, Attention deficit hyperactivity disorder, Moderate global developmental delay

Mean Coverage : 78 %

#4 : pathogenic
Location : 46,241,892 - 51,829,561 | Size : 5,587,669 bases

Patient Id : 295573
Gender : Inconnu
Phenotype : Moderate global developmental delay

Mean Coverage : 78 %

#5 : uncertain
Location : 46,264,301 - 51,780,909 | Size : 5,516,608 bases

Patient Id : 410947
Gender : Inconnu
Phenotype : Autistic behavior, Loss of speech

Mean Coverage : 78 %

#6 : pathogenic
Location : 46,241,892 - 52,000,417 | Size : 5,758,525 bases

Patient Id : 295572
Gender : Inconnu
Phenotype : Joint hypermobility, Short stature, Dyslexia, Moderate global developmental delay

Mean Coverage : 77 %

#7 : unknown
Location : 46,283,685 - 51,822,906 | Size : 5,539,221 bases

Patient Id : 259254
Gender : Inconnu
Phenotype : Low\-set ears, Blepharophimosis, Pectus carinatum, Gynecomastia, Single transverse palmar crease, Hypotonia, Short stature

Mean Coverage : 77 %

#8 : pathogenic
Location : 46,287,820 - 51,861,466 | Size : 5,573,646 bases

Patient Id : 327088
Gender : Inconnu
Phenotype : Protruding ear, Congenital nystagmus, Uplifted earlobe, Unilateral microphthalmos, Anteverted ears

Mean Coverage : 77 %

#9 : unknown
Location : 46,287,820 - 51,874,356 | Size : 5,586,536 bases

Patient Id : 263485
Gender : Inconnu

Mean Coverage : 77 %

#10 : unknown
Location : 46,405,261 - 51,780,901 | Size : 5,375,640 bases

Patient Id : 260106
Gender : Inconnu
Phenotype : Impaired social interactions, Specific learning disability, Cognitive impairment

Mean Coverage : 76 %

#11 : unknown
Location : 46,342,336 - 52,020,271 | Size : 5,677,935 bases

Patient Id : 273399
Gender : Inconnu
Phenotype : High palate, Short philtrum, Low\-set ears, Abnormality of the pinna, Strabismus, Myopia, Soft skin, Seizure, Intellectual disability, moderate, Inverted nipples, Posterior plagiocephaly, Anteverted ears

Mean Coverage : 75 %

#12 : uncertain
Location : 46,215,429 - 52,467,181 | Size : 6,251,752 bases

Patient Id : 402953
Gender : Inconnu

Mean Coverage : 73 %

#13 : uncertain
Location : 46,215,429 - 52,467,181 | Size : 6,251,752 bases

Patient Id : 404263
Gender : Inconnu

Mean Coverage : 73 %

1 Gene(s) in SFARI Database

WDFY4 SFARI Location : 49,892,918 - 50,191,001 | Size : 298,083 bases
Exons 1->1 / 62

No data about Syndromicity

Gene Score : 2
Reports : 8

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

DGV-Gold #1
Location : 46,719,449 - 49,176,867 | Size : 2,457,418 bases

Frequency in Population : 3.17 %
Inner Rank : 9

Mean Coverage : 79 %

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

DGV #1
Location : 46,680,255 - 49,378,479 | Size : 2,698,224 bases

Mean Coverage : 83 %

1 Patient cases (>= 70% only)

47,006,953 - 51,330,432
Size : 4,323,479 bases
7 Reports

Mean Coverage : 71 %

1 Controls (>= 70% only)

nssv3707830
Location : 46527664 - 51911841 | Size : 5384177 bases

Mean Coverage : 73 %

4 Gene(s) in PanelApp Database

MAPK8 PanelApp Exons 1->12 / 12 - Size : 132,721 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
Low	Primary immunodeficiency or monogenic inflammatory bowel disease	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	- chronic mucocutaneous candidiasis - connective tissue disorders	- Expert Review Red - Literature

SYT15 PanelApp Whole gene - Size : 15,956 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
Low	Congenital myaesthenic syndrome			- Expert Review Red - NHS GMS - Wessex and West Midlands GLH

RBP3 PanelApp Whole gene - Size : 9,518 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
Low	Glaucoma (developmental)		- Eye Disorders	- NHS GMS - Emory Genetics Laboratory
High	Retinal disorders	BIALLELIC, autosomal or pseudoautosomal	- Eye Disorders - Retinitis Pigmentosa, Recessive - Retinitis pigmentosa - ?Retinitis pigmentosa 66, 615233	- NHS GMS - Expert Review Green
Low	Structural eye disease	BIALLELIC, autosomal or pseudoautosomal	- ?Retinitis pigmentosa 66, 615233 - Eye Disorders	- NHS GMS - Expert Review Red

GDF2 PanelApp Whole gene - Size : 5,134 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
Medium	Cerebral vascular malformations	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	- Telangiectasia, hereditary hemorrhagic, type 5, OMIM:615506	- Yorkshire and North East GLH - NHS GMS - Expert Review Amber - Radboud University Medical Center, Nijmegen - UKGTN - Emory Genetics Laboratory
High	Hereditary haemorrhagic telangiectasia	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	- Telangiectasia, hereditary hemorrhagic, type 5 OMIM:615506 - telangiectasia, hereditary hemorrhagic, type 5 MONDO:0014217	- Expert Review Green - NHS GMS - Expert Review - Radboud University Medical Center, Nijmegen - UKGTN - Emory Genetics Laboratory
High	Pulmonary arterial hypertension	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	- Heritable pulmonary arterial hypertension - HPAH	- NHS GMS - Expert Review Green - Literature
Low	Fetal anomalies	BIALLELIC, autosomal or pseudoautosomal	- Lymphatic dysplasia - hydrothorax - hydrops	- Expert Review Red - Literature

ClassifyCNV ACMG Score

Uncertain

ClassifyCNV ACMG Criteria

2H
+ 0.15

Multiple HI predictors suggest that AT LEAST ONE gene in the interval is haploinsufficient (HI).

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.

3C
+ 0.9

Number of protein-coding RefSeq genes wholly or partially included in the CNV 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) : 3,800,000 bases - Length (hg38) : 3,087,403 bases

CNV-Hub AChro-PuceUncertain

AChro-Puce Criteria taken into account 1

2 Major

2 Major

2 Minor

4 Major

4 Major

4 Minor

4 Minor

ISV 2

XCNV 3

ClassifyCNV ACMG 4

AnnotSV ACMG 5

ACMG criteria

ClassifyCNV

2H + 0.15

5B -0.45

5D + 0.45

AnnotSV

2A + 1

3C + 0.9

5B -0.45

5D + 0.45

ClinGen

Decipher

DGV-Gold

0

0

DGV

1

1

Coe & Al study 6

1

1

Genes with pHaplo > 0.55 7

2

Genes with pTriplo > 0.68 7

1

Genes in SFARI

1

Genes in OMIM

12

Sources and references

12 OMIM Gene overlap(s)

Download genes as .csv

WDFY4 NM_001394531.1 Exons 1->1 / 62 - Size : 298,083 bases

Database :

SFARI (Autism Database) :

ARHGAP22 NM_021226.4 Exons 1->10 / 10 - Size : 210,231 bases

Database :

MAPK8 NM_001323329.2 Exons 1->12 / 12 - Size : 132,721 bases

Database :

Human Phenotype Ontology Show/Hide

FRMPD2 NM_001018071.4 Exons 1->29 / 29 - Size : 121,608 bases

Database :

WASHC2C NM_001330074.2 Whole gene - Size : 65,764 bases

Database :

ANXA8 NM_001040084.3 Whole gene - Size : 23,996 bases

Database :

SYT15 NM_031912.5 Whole gene - Size : 15,956 bases

Database :

GPRIN2 NM_001385282.1 Whole gene - Size : 14,922 bases

Database :

GDF10 NM_004962.5 Whole gene - Size : 13,380 bases

Database :

RBP3 NM_002900.3 Whole gene - Size : 9,518 bases

Database :

Human Phenotype Ontology Show/Hide

GDF2 NM_016204.4 Whole gene - Size : 5,134 bases

Database :

Human Phenotype Ontology Show/Hide

NPY4R NM_005972.6 Whole gene - Size : 4,863 bases

Database :

104 Non-OMIM Gene overlap(s)

NOVELSize : 162,265 bases

ENSG00000289143Size : 130,349 bases

KNOWNSize : 91,090 bases

KNOWNSize : 91,092 bases

ENSG00000289444Size : 103,796 bases

CNV-Hub AChro-Puce
Uncertain

AChro-Puce Criteria taken into account¹

ISV²

XCNV³

ClassifyCNV ACMG⁴

AnnotSV ACMG⁵

2H
+ 0.15

5B
-0.45

5D
+ 0.45

2A
+ 1

3C
+ 0.9

5B
-0.45

5D
+ 0.45

Coe & Al study⁶

Genes with pHaplo > 0.55⁷

Genes with pTriplo > 0.68⁷

NOVEL
Size : 162,265 bases

ENSG00000289143
Size : 130,349 bases

KNOWN
Size : 91,090 bases

KNOWN
Size : 91,092 bases

ENSG00000289444
Size : 103,796 bases

ZFAND4
Size : 57,280 bases

KNOWN
Size : 62,078 bases

KNOWN
Size : 55,389 bases

KNOWN
Size : 53,415 bases

KNOWN
Size : 49,870 bases

PTPN20CP
Size : 55,150 bases

KNOWN
Size : 47,894 bases

NOVEL
Size : 35,697 bases

KNOWN
Size : 40,985 bases

ANTXRLP1
Size : 39,672 bases

ANTXRL
Size : 43,862 bases

FAM245B
Size : 30,723 bases

KNOWN
Size : 47,896 bases

LINC02675
Size : 30,813 bases

ENSG00000290899
Size : 34,945 bases

AGAP10P
Size : 21,840 bases

FAM21FP
Size : 16,008 bases

AGAP4
Size : 28,281 bases

KNOWN
Size : 24,468 bases

KNOWN
Size : 15,946 bases

KNOWN
Size : 23,593 bases

SHLD2P1
Size : 20,974 bases

ENSG00000229227
Size : 14,236 bases

SYT15-AS1
Size : 17,442 bases

SYT15B
Size : 18,889 bases

KNOWN
Size : 16,110 bases

KNOWN
Size : 13,576 bases

NOVEL
Size : 10,760 bases

AGAP14P
Size : 21,480 bases

ENSG00000279458
Size : 11,909 bases

KNOWN
Size : 16,105 bases

NOVEL
Size : 23,909 bases

KNOWN
Size : 11,840 bases

KNOWN
Size : 12,880 bases

NOVEL
Size : 23,920 bases

ZNF488
Size : 18,797 bases

ENSG00000289299
Size : 17,549 bases

KNOWN
Size : 24,468 bases

KNOWN
Size : 27,778 bases

AGAP12P
Size : 21,719 bases

AGAP12P
Size : 21,501 bases

BMS1P7
Size : 9,756 bases

ENSG00000290460
Size : 9,205 bases

ENSG00000228702
Size : 344 bases

ENSG00000270434
Size : 296 bases

FAM25E
Size : 1,896 bases

FAM25E
Size : 1,763 bases

RNA5SP310
Size : 115 bases

KNOWN
Size : 115 bases

KNOWN
Size : 6,100 bases

KNOWN
Size : 1,759 bases

KNOWN
Size : 1,118 bases

KNOWN
Size : 283 bases

LINC02637
Size : 3,085 bases

RHEBP1
Size : 555 bases

ENSG00000290913
Size : 9,216 bases

NPY4R2
Size : 4,863 bases

HNRNPA1P33
Size : 560 bases

ENSG00000273760
Size : 3,451 bases