hg19 GAIN chrX-6441957-8167697

Length (hg19) : 1,725,740 bases - Length (hg38) : 1,675,740 bases

French Guidelines of the AChro-Puce Network
Likely benign

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.
LIKELY BENIGN (Benign if the patient is female)

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 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

CNV length of 1 Mb or more

ISV²

XCNV³

ClassifyCNV ACMG⁴

AnnotSV ACMG⁵

ACMG criteria

ClassifyCNV

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
STS	Recessive X-linked ichthyosis	Orphanet	X-linked recessive

ClinGen

19 benign CNV
6 likely benign CNV
20 uncertain CNV
6 likely pathogenic CNV
3 pathogenic CNV

70% Overlaps

DGV-Gold

0

80% Overlaps

0

50% Overlaps

DGV

0

80% Overlaps

3

50% Overlaps

Coe & Al study⁶

0

Patient cases
70% Overlaps

0

Controls
70% Overlaps

Genes with pTriplo > 0.68⁷

0 Genes with pHaplo > 0.55⁷

0 Genes in SFARI

0 Genes in OMIM

6 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

Not Working? You Can Delete and Recompute the CNV

1 Microdeletion and microduplication syndromes from litterature (>= 70% only)

STS (Xp22.31)
Location : 6,455,812 - 8,124,954 | Size : 1,669,142 bases

Cases :
Shapiro_1989
Alperin_1997
Valdes-Flores_2000
Hand_2014
Brcic_2020
Gubb_2020

Mean Coverage : 98 %

6 OMIM Gene overlap(s)

Download genes as .csv

STS NM_001320752.2 Whole gene - Size : 707,121 bases

pLI : 0.81 LOEUF : 0.44 sHet : 0.19
Location : 7,065,278 - 7,772,399

Disease : Recessive X-linked ichthyosis

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:300747 Orphanet:461 HGNC:11425 PMID:10583107 PMID:1069212 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:0003623	Neonatal onset	Onset of signs or symptoms of disease within the first 28 days of life.
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:0007431	Congenital ichthyosiform erythroderma	An ichthyosiform abnormality of the skin with congenital onset.
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: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:0000083	Renal insufficiency	A reduction in the level of performance of the kidneys in areas of function comprising the concentration of urine, removal of wastes, the maintenance of electrolyte balance, homeostasis of blood pressure, and calcium metabolism.
HP:0001339	Lissencephaly	A spectrum of malformations of cortical development caused by insufficient neuronal migration that subsumes the terms agyria, pachygyria and subcortical band heterotopia. See also neuropathological definitions for 2-, 3-, and 4-layered lissencephaly.
HP:0000028	Cryptorchidism	Testis in inguinal canal. That is, absence of one or both testes from the scrotum owing to failure of the testis or testes to descend through the inguinal canal to the scrotum.
HP:0100617	Testicular seminoma	The presence of a seminoma, an undifferentiated germ cell tumor of the testis.
HP:0033252	Palmar hyperlinearity	Exaggerated skin markings (dermatoglyphics) on the palms of the hand.
HP:0003577	Congenital onset	A phenotypic abnormality that is present at birth.
HP:0010866	Abdominal wall defect	An incomplete closure of the abdominal wall.
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:0000962	Hyperkeratosis	Hyperkeratosis is thickening of the outer layer of the skin, the stratum corneum, which is composed of large, polyhedral, plate-like envelopes filled with keratin which are the dead cells that have migrated up from the stratum granulosum.
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:0008064	Ichthyosis	An abnormality of the skin characterized the presence of excessive amounts of dry surface scales on the skin resulting from an abnormality of keratinization.
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:0010788	Testicular neoplasm	The presence of a neoplasm of the testis.
HP:0002488	Acute leukemia	A clonal (malignant) hematopoietic disorder with an acute onset, affecting the bone marrow and the peripheral blood. The malignant cells show minimal differentiation and are called blasts, either myeloid blasts (myeloblasts) or lymphoid blasts (lymphoblasts).
HP:0000982	Palmoplantar keratoderma	Abnormal thickening of the skin of the palms of the hands and the soles of the feet.
HP:0011463	Childhood onset	Onset of disease at the age of between 1 and 5 years.
HP:0000122	Unilateral renal agenesis	A unilateral form of agenesis of the kidney.
HP:0002381	Aphasia	An acquired language impairment of some or all of the abilities to produce or comprehend speech and to read or write.
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:0007957	Corneal opacity	A reduction of corneal clarity.
HP:0000958	Dry skin	Skin characterized by the lack of natural or normal moisture.
HP:0007759	Opacification of the corneal stroma	Reduced transparency of the stroma of cornea.
HP:0002167	Abnormality of speech or vocalization	Abnormalities in the sound of a person's speech or vocalization are not necessarily associated with a known physical cause or due to stuttering or stammering.
HP:0000966	Hypohidrosis	Abnormally diminished capacity to sweat.
HP:0002577	Abnormal stomach morphology	An abnormality of the stomach.
HP:0004298	Abnormality of the abdominal wall	The presence of any abnormality affecting the abdominal wall.
HP:0000135	Hypogonadism	A decreased functionality of the gonad.

PUDP NM_012080.5 Whole gene - Size : 480,293 bases

pLI : 0.32 LOEUF : 1.11
Location : 6,585,906 - 7,066,199

Database :

DecipherGenomics PanelApp OMIM:306480 GTEx Portal Human Protein Atlas Ensembl

PNPLA4 NM_004650.3 Whole gene - Size : 29,492 bases

pLI : 0 LOEUF : 1.27 sHet : 0.017
Location : 7,866,288 - 7,895,780

Database :

DecipherGenomics PanelApp OMIM:300102 GTEx Portal Human Protein Atlas Ensembl

VCX NM_001393662.1 Whole gene - Size : 1,881 bases

pLI : 0.34 LOEUF : 1.82
Location : 7,810,303 - 7,812,184

Database :

DecipherGenomics OMIM:300229 GTEx Portal Human Protein Atlas Ensembl

VCX3A NM_016379.4 Whole gene - Size : 1,500 bases

pLI : 0.31 LOEUF : 1.87
Location : 6,451,659 - 6,453,159

Database :

DecipherGenomics OMIM:300533 GTEx Portal Human Protein Atlas Ensembl

VCX2 NM_016378.3 Whole gene - Size : 1,323 bases

pLI : 0.06 LOEUF : 1.94
Location : 8,137,985 - 8,139,308

Database :

DecipherGenomics OMIM:300532 GTEx Portal Human Protein Atlas Ensembl

7 Non-OMIM Gene overlap(s)

ENSG00000285679
Size : 445,943 bases

Location : 7,896,484 - 8,342,427

RPS27AP17
Size : 454 bases

Location : 6,907,370 - 6,907,824

ENSG00000279682
Size : 1,540 bases

Location : 7,407,700 - 7,409,240

ENSG00000274923
Size : 208 bases

Location : 7,864,555 - 7,864,763

KNOWN
Size : 77 bases

Location : 7,065,901 - 7,065,978

KNOWN
Size : 96 bases

Location : 8,095,006 - 8,095,102

ENSG00000228550
Size : 399 bases

Location : 7,031,046 - 7,031,445

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

19 Benign CNV 6 Likely benign CNV 20 Uncertain CNV 6 Likely pathogenic CNV 3 Pathogenic CNV

#1 Uncertain significance (Xp22.31)
Location : 6,442,424 - 8,135,239 | Size : 1,692,815 bases

Score : 0

Mean Coverage : 99 %

#2 Likely pathogenic (Xp22.31)
Location : 6,450,699 - 8,138,035 | Size : 1,687,336 bases

Score : 1

Mean Coverage : 99 %

#3 Uncertain significance (Xp22.31)
Location : 6,449,751 - 8,135,645 | Size : 1,685,894 bases

Score : 0

Mean Coverage : 99 %

#4 Uncertain significance (Xp22.31)
Location : 6,454,812 - 8,139,581 | Size : 1,684,769 bases

Score : 0

Mean Coverage : 99 %

#5 Likely benign (nssv13648739)
Location : 6,453,035 - 8,131,751 | Size : 1,678,716 bases

Score : 0

Mean Coverage : 99 %

#6 Uncertain significance (Xp22.31)
Location : 6,454,812 - 8,135,239 | Size : 1,680,427 bases

Score : 0

Mean Coverage : 99 %

#7 Pathogenic (Xp22.31)
Location : 6,448,750 - 8,135,644 | Size : 1,686,894 bases

Score : 0

Mean Coverage : 99 %

#8 Uncertain significance (Xp22.31)
Location : 6,448,750 - 8,135,644 | Size : 1,686,894 bases

Score : 0

Mean Coverage : 99 %

#9 Likely benign (Xp22.31)
Location : 6,445,320 - 8,152,874 | Size : 1,707,554 bases

Score : 0
Phenotype : Global developmental delay

Mean Coverage : 99 %

#10 Uncertain significance (Single allele)
Location : 6,456,035 - 8,133,172 | Size : 1,677,137 bases

Score : 1
Phenotype : Primary amenorrhea

Mean Coverage : 99 %

#11 Uncertain significance (Xp22.31)
Location : 6,429,318 - 8,135,644 | Size : 1,706,326 bases

Score : 0

Mean Coverage : 99 %

#12 Uncertain significance (Xp22.31)
Location : 6,453,208 - 8,132,826 | Size : 1,679,618 bases

Score : 1

Mean Coverage : 99 %

#13 Uncertain significance (Xp22.31)
Location : 6,454,812 - 8,135,053 | Size : 1,680,241 bases

Score : 0

Mean Coverage : 99 %

#14 Uncertain significance (Xp22.31)
Location : 6,449,232 - 8,135,644 | Size : 1,686,412 bases

Score : 0

Mean Coverage : 99 %

#15 Likely pathogenic (Xp22.31)
Location : 6,458,165 - 8,135,053 | Size : 1,676,888 bases

Score : 1

Mean Coverage : 99 %

#16 Uncertain significance (Xp22.31)
Location : 6,446,824 - 8,144,888 | Size : 1,698,064 bases

Score : 0

Mean Coverage : 99 %

#17 Benign (nssv13645575)
Location : 6,453,035 - 8,139,186 | Size : 1,686,151 bases

Score : 0

Mean Coverage : 99 %

#18 Benign (Xp22.31)
Location : 6,456,939 - 8,135,053 | Size : 1,678,114 bases

Score : 0

Mean Coverage : 99 %

#19 Benign (nssv579577)
Location : 6,452,206 - 8,136,721 | Size : 1,684,515 bases

Score : 1

Mean Coverage : 99 %

#20 Uncertain significance (Single allele)
Location : 6,453,035 - 8,139,238 | Size : 1,686,203 bases

Score : 1

Mean Coverage : 99 %

#21 Likely benign (nssv13652011)
Location : 6,453,035 - 8,151,615 | Size : 1,698,580 bases

Score : 0

Mean Coverage : 99 %

#22 Likely benign (nssv13653488)
Location : 6,453,035 - 8,151,615 | Size : 1,698,580 bases

Score : 0

Mean Coverage : 99 %

#23 Likely pathogenic (Xp22.31)
Location : 6,476,349 - 8,135,053 | Size : 1,658,704 bases

Score : 1

Mean Coverage : 98 %

#24 Benign (nssv706907)
Location : 6,452,680 - 8,097,511 | Size : 1,644,831 bases

Score : 0

Mean Coverage : 98 %

#25 Benign (nssv1601836)
Location : 6,452,680 - 8,097,511 | Size : 1,644,831 bases

Score : 0

Mean Coverage : 98 %

#26 Likely benign (nssv1608353)
Location : 6,450,427 - 8,115,094 | Size : 1,664,667 bases

Score : 0

Mean Coverage : 98 %

#27 Likely benign (nssv1609818)
Location : 6,449,687 - 8,115,094 | Size : 1,665,407 bases

Score : 0

Mean Coverage : 98 %

#28 Benign (nssv1608327)
Location : 6,449,687 - 8,115,094 | Size : 1,665,407 bases

Score : 0

Mean Coverage : 98 %

#29 Benign (nssv1609744)
Location : 6,454,211 - 8,115,094 | Size : 1,660,883 bases

Score : 0

Mean Coverage : 98 %

#30 Likely pathogenic (Xp22.31)
Location : 6,477,549 - 8,119,329 | Size : 1,641,780 bases

Score : 1

Mean Coverage : 98 %

#31 Benign (nssv1602864)
Location : 6,452,694 - 8,097,511 | Size : 1,644,817 bases

Score : 0

Mean Coverage : 98 %

#32 Benign (nssv579581)
Location : 6,467,005 - 8,115,153 | Size : 1,648,148 bases

Score : 1

Mean Coverage : 98 %

#33 Uncertain significance (Xp22.31)
Location : 6,455,150 - 8,128,200 | Size : 1,673,050 bases

Score : 0

Mean Coverage : 98 %

#34 Benign (nssv1603833)
Location : 6,453,048 - 8,097,511 | Size : 1,644,463 bases

Score : 0

Mean Coverage : 98 %

#35 Benign (nssv579578)
Location : 6,452,206 - 8,116,067 | Size : 1,663,861 bases

Score : 1

Mean Coverage : 98 %

#36 Uncertain significance (Xp22.31)
Location : 6,516,734 - 8,135,053 | Size : 1,618,319 bases

Score : 1
Phenotype : Premature ovarian failure

Mean Coverage : 97 %

#37 Uncertain significance (Xp22.31)
Location : 6,500,764 - 8,135,644 | Size : 1,634,880 bases

Score : 0

Mean Coverage : 97 %

#38 Uncertain significance (nssv3396104)
Location : 6,488,720 - 8,097,511 | Size : 1,608,791 bases

Score : 0

Mean Coverage : 96 %

#39 Benign (nssv576505)
Location : 6,488,720 - 8,097,511 | Size : 1,608,791 bases

Score : 0

Mean Coverage : 96 %

#40 Benign (nssv579580)
Location : 6,457,402 - 8,032,120 | Size : 1,574,718 bases

Score : 1

Mean Coverage : 95 %

#41 Benign (nssv579579)
Location : 6,457,402 - 8,032,120 | Size : 1,574,718 bases

Score : 1

Mean Coverage : 95 %

#42 Benign (nssv579584)
Location : 6,488,720 - 8,050,650 | Size : 1,561,930 bases

Score : 1

Mean Coverage : 95 %

#43 Benign (nssv579583)
Location : 6,488,720 - 8,050,650 | Size : 1,561,930 bases

Score : 1

Mean Coverage : 95 %

#44 Likely pathogenic (Xp22.31)
Location : 6,596,638 - 8,135,053 | Size : 1,538,415 bases

Score : 1

Mean Coverage : 94 %

#45 Uncertain significance (nssv3396085)
Location : 6,570,936 - 8,097,511 | Size : 1,526,575 bases

Score : 0

Mean Coverage : 94 %

#46 Uncertain significance (Xp22.31)
Location : 6,631,976 - 8,135,644 | Size : 1,503,668 bases

Score : 0

Mean Coverage : 93 %

#47 Pathogenic (nssv582313)
Location : 6,628,263 - 8,097,511 | Size : 1,469,248 bases

Score : 0

Mean Coverage : 92 %

#48 Pathogenic (Xp22.31)
Location : 6,677,960 - 8,144,721 | Size : 1,466,761 bases

Score : 0

Mean Coverage : 92 %

#49 Benign (nssv1604450)
Location : 6,452,694 - 8,497,777 | Size : 2,045,083 bases

Score : 0

Mean Coverage : 91 %

#50 Uncertain significance (Xp22.31)
Location : 6,112,443 - 8,257,510 | Size : 2,145,067 bases

Score : 0

Mean Coverage : 89 %

#51 Benign (nssv576556)
Location : 6,453,071 - 7,809,341 | Size : 1,356,270 bases

Score : 0

Mean Coverage : 88 %

#52 Likely pathogenic (Xp22.31)
Location : 6,179,829 - 8,605,251 | Size : 2,425,422 bases

Score : 1

Mean Coverage : 83 %

#53 Uncertain significance (Xp22.31)
Location : 7,043,619 - 8,050,591 | Size : 1,006,972 bases

Score : 0
Phenotype : Intellectual disability

Mean Coverage : 74 %

#54 Benign (nssv579585)
Location : 6,551,154 - 7,555,351 | Size : 1,004,197 bases

Score : 1

Mean Coverage : 74 %

0 Gene(s) in SFARI Database

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

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

DGV #1
Location : 6,455,152 - 7,120,567 | Size : 665,415 bases

Mean Coverage : 56 %

DGV #2
Location : 7,399,834 - 8,002,862 | Size : 603,028 bases

Mean Coverage : 52 %

DGV #3
Location : 7,514,751 - 8,135,644 | Size : 620,893 bases

Mean Coverage : 53 %

0 Patient cases (>= 70% only)

0 Controls (>= 70% only)

3 Gene(s) in PanelApp Database

STS PanelApp Whole gene - Size : 707,121 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
High	Autosomal recessive congenital ichthyosis	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	- Ichthyosis, X-linked, 308100	- Expert Review Green - Radboud University Medical Center, Nijmegen - UKGTN - Eligibility statement prior genetic testing
High	Ichthyosis and erythrokeratoderma	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	- Ichthyosis, X-linked, OMIM:308100	- Expert Review Green
High	Palmoplantar keratodermas	X-LINKED: hemizygous mutation in males, biallelic mutations in females	- X linked ichthyosis	- London North GLH - NHS GMS - Expert Review Green
High	Corneal dystrophy	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	- Ichthyosis, X-linked	- Expert Review Green - Wessex and West Midlands GLH
High	Undiagnosed metabolic disorders	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	- X-linked ichthyosis (Other disorders in the metabolism of sterols) - Autosomal recessive congenital ichthyosis	- Expert Review Green - Literature
High	Likely inborn error of metabolism - targeted testing not possible	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	- X-linked ichthyosis (Other disorders in the metabolism of sterols) - Autosomal recessive congenital ichthyosis	- Expert Review Green - London North GLH - NHS GMS
Low	Fetal anomalies	X-LINKED: hemizygous mutation in males, biallelic mutations in females	- ICHTHYOSIS, X-LINKED	- Expert Review Red - PAGE DD-Gene2Phenotype
High	DDG2P	X-LINKED: hemizygous mutation in males, biallelic mutations in females	- ICHTHYOSIS, X-LINKED 308100	- DD-Gene2Phenotype - Expert Review Green
Low	Intellectual disability - microarray and sequencing	X-LINKED: hemizygous mutation in males, biallelic mutations in females	- Gene2Phenotype confirmed gene with ID HPO	- Expert Review Red - BRIDGE study SPEED NEURO Tier1 Gene
Low	Childhood onset dystonia, chorea or related movement disorder			- Expert Review Red - London North GLH
Low	Childhood onset dystonia, chorea or related movement disorder			- Expert Review Red - London North GLH

PUDP PanelApp Whole gene - Size : 480,293 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
Low	Intellectual disability - microarray and sequencing	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)		- Expert Review Red

PNPLA4 PanelApp Whole gene - Size : 29,492 bases

Confidence	Disease	Inheritance	Phenotype	Evidence
Low	Likely inborn error of metabolism - targeted testing not possible	Unknown		- Expert Review Red
Low	Possible mitochondrial disorder - nuclear genes	X-LINKED: hemizygous mutation in males, biallelic mutations in females	- No OMIM phenotype	- NHS GMS - Expert Review Red
Low	Mitochondrial disorders			- Victorian Clinical Genetics Services

ClassifyCNV ACMG Score

Uncertain

ClassifyCNV ACMG Criteria

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) : 1,725,740 bases - Length (hg38) : 1,675,740 bases

French Guidelines of the AChro-Puce NetworkLikely benign

AChro-Puce Criteria taken into account 1

2 Major

2 Minor

4 Major

4 Major

4 Minor

ISV 2

XCNV 3

ClassifyCNV ACMG 4

AnnotSV ACMG 5

ACMG criteria

ClassifyCNV

5B -0.45

5D + 0.45

AnnotSV

2A + 1

5B -0.45

5D + 0.45

Diseases :

ClinGen

DGV-Gold

0

0

DGV

0

3

Coe & Al study 6

0

0

Genes with pTriplo > 0.68 7

0

Genes with pHaplo > 0.55 7

0

Genes in SFARI

0

Genes in OMIM

6

Sources and references

1 Microdeletion and microduplication syndromes from litterature (>= 70% only)

STS (Xp22.31) Location : 6,455,812 - 8,124,954 | Size : 1,669,142 bases

6 OMIM Gene overlap(s)

Download genes as .csv

STS NM_001320752.2 Whole gene - Size : 707,121 bases

Disease : Recessive X-linked ichthyosis

Source : Orphanet

Database :

Human Phenotype Ontology Show/Hide

PUDP NM_012080.5 Whole gene - Size : 480,293 bases

Database :

PNPLA4 NM_004650.3 Whole gene - Size : 29,492 bases

Database :

VCX NM_001393662.1 Whole gene - Size : 1,881 bases

Database :

VCX3A NM_016379.4 Whole gene - Size : 1,500 bases

Database :

VCX2 NM_016378.3 Whole gene - Size : 1,323 bases

Database :

7 Non-OMIM Gene overlap(s)

ENSG00000285679Size : 445,943 bases

RPS27AP17Size : 454 bases

ENSG00000279682Size : 1,540 bases

ENSG00000274923Size : 208 bases

KNOWNSize : 77 bases

KNOWNSize : 96 bases

ENSG00000228550Size : 399 bases

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

#1 Uncertain significance (Xp22.31) Location : 6,442,424 - 8,135,239 | Size : 1,692,815 bases

#2 Likely pathogenic (Xp22.31) Location : 6,450,699 - 8,138,035 | Size : 1,687,336 bases

#3 Uncertain significance (Xp22.31) Location : 6,449,751 - 8,135,645 | Size : 1,685,894 bases

#4 Uncertain significance (Xp22.31) Location : 6,454,812 - 8,139,581 | Size : 1,684,769 bases

#5 Likely benign (nssv13648739) Location : 6,453,035 - 8,131,751 | Size : 1,678,716 bases

#6 Uncertain significance (Xp22.31) Location : 6,454,812 - 8,135,239 | Size : 1,680,427 bases

#7 Pathogenic (Xp22.31) Location : 6,448,750 - 8,135,644 | Size : 1,686,894 bases

#8 Uncertain significance (Xp22.31) Location : 6,448,750 - 8,135,644 | Size : 1,686,894 bases

#9 Likely benign (Xp22.31) Location : 6,445,320 - 8,152,874 | Size : 1,707,554 bases

#10 Uncertain significance (Single allele) Location : 6,456,035 - 8,133,172 | Size : 1,677,137 bases

#11 Uncertain significance (Xp22.31) Location : 6,429,318 - 8,135,644 | Size : 1,706,326 bases

#12 Uncertain significance (Xp22.31) Location : 6,453,208 - 8,132,826 | Size : 1,679,618 bases

French Guidelines of the AChro-Puce Network
Likely benign

AChro-Puce Criteria taken into account¹

ISV²

XCNV³

ClassifyCNV ACMG⁴

AnnotSV ACMG⁵

5B
-0.45

5D
+ 0.45

2A
+ 1

5B
-0.45

5D
+ 0.45

Coe & Al study⁶

Genes with pTriplo > 0.68⁷

Genes with pHaplo > 0.55⁷

STS (Xp22.31)
Location : 6,455,812 - 8,124,954 | Size : 1,669,142 bases

ENSG00000285679
Size : 445,943 bases

RPS27AP17
Size : 454 bases

ENSG00000279682
Size : 1,540 bases

ENSG00000274923
Size : 208 bases

KNOWN
Size : 77 bases

KNOWN
Size : 96 bases

ENSG00000228550
Size : 399 bases

#1 Uncertain significance (Xp22.31)
Location : 6,442,424 - 8,135,239 | Size : 1,692,815 bases

#2 Likely pathogenic (Xp22.31)
Location : 6,450,699 - 8,138,035 | Size : 1,687,336 bases

#3 Uncertain significance (Xp22.31)
Location : 6,449,751 - 8,135,645 | Size : 1,685,894 bases

#4 Uncertain significance (Xp22.31)
Location : 6,454,812 - 8,139,581 | Size : 1,684,769 bases

#5 Likely benign (nssv13648739)
Location : 6,453,035 - 8,131,751 | Size : 1,678,716 bases

#6 Uncertain significance (Xp22.31)
Location : 6,454,812 - 8,135,239 | Size : 1,680,427 bases

#7 Pathogenic (Xp22.31)
Location : 6,448,750 - 8,135,644 | Size : 1,686,894 bases

#8 Uncertain significance (Xp22.31)
Location : 6,448,750 - 8,135,644 | Size : 1,686,894 bases

#9 Likely benign (Xp22.31)
Location : 6,445,320 - 8,152,874 | Size : 1,707,554 bases

#10 Uncertain significance (Single allele)
Location : 6,456,035 - 8,133,172 | Size : 1,677,137 bases

#11 Uncertain significance (Xp22.31)
Location : 6,429,318 - 8,135,644 | Size : 1,706,326 bases

#12 Uncertain significance (Xp22.31)
Location : 6,453,208 - 8,132,826 | Size : 1,679,618 bases

#13 Uncertain significance (Xp22.31)
Location : 6,454,812 - 8,135,053 | Size : 1,680,241 bases

#14 Uncertain significance (Xp22.31)
Location : 6,449,232 - 8,135,644 | Size : 1,686,412 bases

#15 Likely pathogenic (Xp22.31)
Location : 6,458,165 - 8,135,053 | Size : 1,676,888 bases

#16 Uncertain significance (Xp22.31)
Location : 6,446,824 - 8,144,888 | Size : 1,698,064 bases

#17 Benign (nssv13645575)
Location : 6,453,035 - 8,139,186 | Size : 1,686,151 bases

#18 Benign (Xp22.31)
Location : 6,456,939 - 8,135,053 | Size : 1,678,114 bases

#19 Benign (nssv579577)
Location : 6,452,206 - 8,136,721 | Size : 1,684,515 bases

#20 Uncertain significance (Single allele)
Location : 6,453,035 - 8,139,238 | Size : 1,686,203 bases

#21 Likely benign (nssv13652011)
Location : 6,453,035 - 8,151,615 | Size : 1,698,580 bases

#22 Likely benign (nssv13653488)
Location : 6,453,035 - 8,151,615 | Size : 1,698,580 bases

#23 Likely pathogenic (Xp22.31)
Location : 6,476,349 - 8,135,053 | Size : 1,658,704 bases

#24 Benign (nssv706907)
Location : 6,452,680 - 8,097,511 | Size : 1,644,831 bases

#25 Benign (nssv1601836)
Location : 6,452,680 - 8,097,511 | Size : 1,644,831 bases

#26 Likely benign (nssv1608353)
Location : 6,450,427 - 8,115,094 | Size : 1,664,667 bases

#27 Likely benign (nssv1609818)
Location : 6,449,687 - 8,115,094 | Size : 1,665,407 bases

#28 Benign (nssv1608327)
Location : 6,449,687 - 8,115,094 | Size : 1,665,407 bases

#29 Benign (nssv1609744)
Location : 6,454,211 - 8,115,094 | Size : 1,660,883 bases

#30 Likely pathogenic (Xp22.31)
Location : 6,477,549 - 8,119,329 | Size : 1,641,780 bases

#31 Benign (nssv1602864)
Location : 6,452,694 - 8,097,511 | Size : 1,644,817 bases

#32 Benign (nssv579581)
Location : 6,467,005 - 8,115,153 | Size : 1,648,148 bases

#33 Uncertain significance (Xp22.31)
Location : 6,455,150 - 8,128,200 | Size : 1,673,050 bases

#34 Benign (nssv1603833)
Location : 6,453,048 - 8,097,511 | Size : 1,644,463 bases

#35 Benign (nssv579578)
Location : 6,452,206 - 8,116,067 | Size : 1,663,861 bases

#36 Uncertain significance (Xp22.31)
Location : 6,516,734 - 8,135,053 | Size : 1,618,319 bases

#37 Uncertain significance (Xp22.31)
Location : 6,500,764 - 8,135,644 | Size : 1,634,880 bases

#38 Uncertain significance (nssv3396104)
Location : 6,488,720 - 8,097,511 | Size : 1,608,791 bases

#39 Benign (nssv576505)
Location : 6,488,720 - 8,097,511 | Size : 1,608,791 bases

#40 Benign (nssv579580)
Location : 6,457,402 - 8,032,120 | Size : 1,574,718 bases

#41 Benign (nssv579579)
Location : 6,457,402 - 8,032,120 | Size : 1,574,718 bases

#42 Benign (nssv579584)
Location : 6,488,720 - 8,050,650 | Size : 1,561,930 bases

#43 Benign (nssv579583)
Location : 6,488,720 - 8,050,650 | Size : 1,561,930 bases

#44 Likely pathogenic (Xp22.31)
Location : 6,596,638 - 8,135,053 | Size : 1,538,415 bases

#45 Uncertain significance (nssv3396085)
Location : 6,570,936 - 8,097,511 | Size : 1,526,575 bases

#46 Uncertain significance (Xp22.31)
Location : 6,631,976 - 8,135,644 | Size : 1,503,668 bases

#47 Pathogenic (nssv582313)
Location : 6,628,263 - 8,097,511 | Size : 1,469,248 bases

#48 Pathogenic (Xp22.31)
Location : 6,677,960 - 8,144,721 | Size : 1,466,761 bases

#49 Benign (nssv1604450)
Location : 6,452,694 - 8,497,777 | Size : 2,045,083 bases

#50 Uncertain significance (Xp22.31)
Location : 6,112,443 - 8,257,510 | Size : 2,145,067 bases

#51 Benign (nssv576556)
Location : 6,453,071 - 7,809,341 | Size : 1,356,270 bases

#52 Likely pathogenic (Xp22.31)
Location : 6,179,829 - 8,605,251 | Size : 2,425,422 bases

#53 Uncertain significance (Xp22.31)
Location : 7,043,619 - 8,050,591 | Size : 1,006,972 bases

#54 Benign (nssv579585)
Location : 6,551,154 - 7,555,351 | Size : 1,004,197 bases

DGV #1
Location : 6,455,152 - 7,120,567 | Size : 665,415 bases

DGV #2
Location : 7,399,834 - 8,002,862 | Size : 603,028 bases

DGV #3
Location : 7,514,751 - 8,135,644 | Size : 620,893 bases

5B
-0.45