GRCh37/hg19 Xp11.4-11.22(chrX:39525562-52832596)x3 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 11, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002474503.1

Allele description [Variation Report for GRCh37/hg19 Xp11.4-11.22(chrX:39525562-52832596)x3]

GRCh37/hg19 Xp11.4-11.22(chrX:39525562-52832596)x3

Genes:

ARAF:A-Raf proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
AKAP4:A-kinase anchoring protein 4 [Gene - OMIM - HGNC]
ATP6AP2:ATPase H+ transporting accessory protein 2 [Gene - OMIM - HGNC]
BCOR:BCL6 corepressor [Gene - OMIM - HGNC]
DDX3X:DEAD-box helicase 3 X-linked [Gene - OMIM - HGNC]
EBP:EBP cholestenol delta-isomerase [Gene - OMIM - HGNC]
EFHC2:EF-hand domain containing 2 [Gene - OMIM - HGNC]
ERAS:ES cell expressed Ras [Gene - OMIM - HGNC]
ELK1:ETS transcription factor ELK1 [Gene - OMIM - HGNC]
FUNDC1:FUN14 domain containing 1 [Gene - OMIM - HGNC]
FTSJ1:FtsJ RNA 2'-O-methyltransferase 1 [Gene - OMIM - HGNC]
GAGE12B:G antigen 12B [Gene - HGNC]
GAGE12C:G antigen 12C [Gene - OMIM - HGNC]
GAGE12D:G antigen 12D [Gene - OMIM - HGNC]
GAGE12E:G antigen 12E [Gene - OMIM - HGNC]
GAGE12F:G antigen 12F [Gene - OMIM - HGNC]
GAGE12G:G antigen 12G [Gene - OMIM - HGNC]
GAGE12H:G antigen 12H [Gene - OMIM - HGNC]
GAGE12I:G antigen 12I [Gene - OMIM - HGNC]
GAGE12J:G antigen 12J [Gene - OMIM - HGNC]
GAGE13:G antigen 13 [Gene - OMIM - HGNC]
GAGE1:G antigen 1 [Gene - OMIM - HGNC]
GAGE2A:G antigen 2A [Gene - OMIM - HGNC]
GAGE2B:G antigen 2B [Gene - OMIM - HGNC]
GAGE2C:G antigen 2C [Gene - OMIM - HGNC]
GAGE2D:G antigen 2D [Gene - OMIM - HGNC]
GAGE2E:G antigen 2E [Gene - OMIM - HGNC]
GAGE8:G antigen 8 [Gene - OMIM - HGNC]
GPR34:G protein-coupled receptor 34 [Gene - OMIM - HGNC]
GPR82:G protein-coupled receptor 82 [Gene - OMIM - HGNC]
GPKOW:G-patch domain and KOW motifs [Gene - OMIM - HGNC]
GSPT2:G1 to S phase transition 2 [Gene - OMIM - HGNC]
GATA1:GATA binding protein 1 [Gene - OMIM - HGNC]
GRIPAP1:GRIP1 associated protein 1 [Gene - OMIM - HGNC]
KRBOX4:KRAB box domain containing 4 [Gene - OMIM - HGNC]
MAGED1:MAGE family member D1 [Gene - OMIM - HGNC]
MAGED4:MAGE family member D4 [Gene - OMIM - HGNC]
MAGED4B:MAGE family member D4B [Gene - OMIM - HGNC]
MAGIX:MAGI family member, X-linked [Gene - HGNC]
NDUFB11:NADH:ubiquinone oxidoreductase subunit B11 [Gene - OMIM - HGNC]
OTUD5:OTU deubiquitinase 5 [Gene - OMIM - HGNC]
PAGE1:PAGE family member 1 [Gene - OMIM - HGNC]
PAGE4:PAGE family member 4 [Gene - OMIM - HGNC]
PRAF2:PRA1 domain family member 2 [Gene - OMIM - HGNC]
PIM2:Pim-2 proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
RBM10:RNA binding motif protein 10 [Gene - OMIM - HGNC]
RBM3:RNA binding motif protein 3 [Gene - OMIM - HGNC]
RP2:RP2 activator of ARL3 GTPase [Gene - OMIM - HGNC]
SPANXN5:SPANX family member N5 [Gene - OMIM - HGNC]
SSX1:SSX family member 1 [Gene - OMIM - HGNC]
SSX2:SSX family member 2 [Gene - OMIM - HGNC]
SSX2B:SSX family member 2B [Gene - HGNC]
SSX3:SSX family member 3 [Gene - OMIM - HGNC]
SSX4:SSX family member 4 [Gene - OMIM - HGNC]
SSX4B:SSX family member 4B [Gene - HGNC]
SSX5:SSX family member 5 [Gene - OMIM - HGNC]
SSX7:SSX family member 7 [Gene - OMIM - HGNC]
SUV39H1:SUV39H1 histone lysine methyltransferase [Gene - OMIM - HGNC]
TBC1D25:TBC1 domain family member 25 [Gene - OMIM - HGNC]
TIMP1:TIMP metallopeptidase inhibitor 1 [Gene - OMIM - HGNC]
WAS:WASP actin nucleation promoting factor [Gene - OMIM - HGNC]
WDR13:WD repeat domain 13 [Gene - OMIM - HGNC]
WDR45:WD repeat domain 45 [Gene - OMIM - HGNC]
XAGE1A:X antigen family member 1A [Gene - OMIM - HGNC]
XAGE1B:X antigen family member 1B [Gene - OMIM - HGNC]
XAGE2:X antigen family member 2 [Gene - OMIM - HGNC]
BMP15:bone morphogenetic protein 15 [Gene - OMIM - HGNC]
CACNA1F:calcium voltage-gated channel subunit alpha1 F [Gene - OMIM - HGNC]
CASK:calcium/calmodulin dependent serine protein kinase [Gene - OMIM - HGNC]
CHST7:carbohydrate sulfotransferase 7 [Gene - OMIM - HGNC]
CLCN5:chloride voltage-gated channel 5 [Gene - OMIM - HGNC]
CXorf38:chromosome X open reading frame 38 [Gene - HGNC]
CCDC120:coiled-coil domain containing 120 [Gene - OMIM - HGNC]
CCDC22:coiled-coil domain containing 22 [Gene - OMIM - HGNC]
CFP:complement factor properdin [Gene - OMIM - HGNC]
CCNB3:cyclin B3 [Gene - OMIM - HGNC]
CDK16:cyclin dependent kinase 16 [Gene - OMIM - HGNC]
DGKK:diacylglycerol kinase kappa [Gene - OMIM - HGNC]
DIPK2B:divergent protein kinase domain 2B [Gene - OMIM - HGNC]
DUSP21:dual specificity phosphatase 21 [Gene - OMIM - HGNC]
FOXP3:forkhead box P3 [Gene - OMIM - HGNC]
GLOD5:glyoxalase domain containing 5 [Gene - HGNC]
HDAC6:histone deacetylase 6 [Gene - OMIM - HGNC]
INE1:inactivation escape 1 [Gene - OMIM - HGNC]
JADE3:jade family PHD finger 3 [Gene - OMIM - HGNC]
LINC01560:long intergenic non-protein coding RNA 1560 [Gene - HGNC]
KDM6A:lysine demethylase 6A [Gene - OMIM - HGNC]
MED14:mediator complex subunit 14 [Gene - OMIM - HGNC]
MIR221:microRNA 221 [Gene - OMIM - HGNC]
MIR222:microRNA 222 [Gene - OMIM - HGNC]
MIR502:microRNA 502 [Gene - OMIM - HGNC]
MIR532:microRNA 532 [Gene - OMIM - HGNC]
MPC1L:mitochondrial pyruvate carrier 1 like [Gene - HGNC]
MAOA:monoamine oxidase A [Gene - OMIM - HGNC]
MAOB:monoamine oxidase B [Gene - OMIM - HGNC]
NDP:norrin cystine knot growth factor NDP [Gene - OMIM - HGNC]
NUDT10:nudix hydrolase 10 [Gene - OMIM - HGNC]
NUDT11:nudix hydrolase 11 [Gene - OMIM - HGNC]
NYX:nyctalopin [Gene - OMIM - HGNC]
PQBP1:polyglutamine binding protein 1 [Gene - OMIM - HGNC]
PORCN:porcupine O-acyltransferase [Gene - OMIM - HGNC]
KCND1:potassium voltage-gated channel subfamily D member 1 [Gene - OMIM - HGNC]
PRICKLE3:prickle planar cell polarity protein 3 [Gene - OMIM - HGNC]
PCSK1N:proprotein convertase subtilisin/kexin type 1 inhibitor [Gene - OMIM - HGNC]
PPP1R3F:protein phosphatase 1 regulatory subunit 3F [Gene - HGNC]
PLP2:proteolipid protein 2 [Gene - OMIM - HGNC]
RGN:regucalcin [Gene - OMIM - HGNC]
SHROOM4:shroom family member 4 [Gene - OMIM - HGNC]
SLC35A2:solute carrier family 35 member A2 [Gene - OMIM - HGNC]
SLC38A5:solute carrier family 38 member 5 [Gene - OMIM - HGNC]
SLC9A7:solute carrier family 9 member A7 [Gene - OMIM - HGNC]
SPACA5:sperm acrosome associated 5 [Gene - OMIM - HGNC]
SPACA5B:sperm acrosome associated 5B [Gene - HGNC]
SYN1:synapsin I [Gene - OMIM - HGNC]
SYP:synaptophysin [Gene - OMIM - HGNC]
TFE3:transcription factor binding to IGHM enhancer 3 [Gene - OMIM - HGNC]
TIMM17B:translocase of inner mitochondrial membrane 17B [Gene - OMIM - HGNC]
UBA1:ubiquitin like modifier activating enzyme 1 [Gene - OMIM - HGNC]
USP11:ubiquitin specific peptidase 11 [Gene - OMIM - HGNC]
USP27X:ubiquitin specific peptidase 27 X-linked [Gene - OMIM - HGNC]
USP9X:ubiquitin specific peptidase 9 X-linked [Gene - OMIM - HGNC]
UXT:ubiquitously expressed prefoldin like chaperone [Gene - OMIM - HGNC]
ZNF157:zinc finger protein 157 [Gene - OMIM - HGNC]
ZNF182:zinc finger protein 182 [Gene - OMIM - HGNC]
ZNF41:zinc finger protein 41 [Gene - OMIM - HGNC]
ZNF630:zinc finger protein 630 [Gene - OMIM - HGNC]
ZNF674:zinc finger protein 674 [Gene - OMIM - HGNC]
ZNF81:zinc finger protein 81 [Gene - OMIM - HGNC]

Variant type:

copy number gain

Cytogenetic location:

Xp11.4-11.22

Genomic location:

ChrX: 39525562 - 52832596 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 Xp11.4-11.22(chrX:39525562-52832596)x3

HGVS:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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zinc finger and BTB domain containing 20, isoform CRA_a [Mus musculus]
zinc finger and BTB domain containing 20, isoform CRA_a [Mus musculus]
gi|148665600|gb|EDK98016.1||gnl|WGS |mCP105025

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002771899	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (May 11, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002771899

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(May 11, 2022)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]

PMID:: 31690835
PMCID:: PMC7313390

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002771899.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The copy number gain of Xp11.4p11.22 involves numerous protein-coding genes, including SHROOM4 (OMIM 300579), FTSJ1 (OMIM 300499), DGKK (OMIM 300837), BMP15 (OMIM 300247), PQBP1 (OMIM 300463), and SLC35A2 (OMIM 314375), and is expected to cause phenotypic and/or developmental abnormalities. This region overlaps a recurrent copy number gain associated with X-linked dominant chromosome Xp11.23-p11.22 duplication syndrome (OMIM 300801). Both males and females with this copy number gain are affected. Common clinical features include mild facial dysmorphism, mild to severe intellectual disability, language impairment, early onset of puberty, and epilepsy. Foot abnormalities, 5th finger clinodactyly, tapering fingers, constipation, and exercise intolerance are also observed (Grams 2016). Several candidate genes have been proposed for these phenotypes: SHROOM4, FTSJ1, and DGKK for intellectual disability, BMP15 for early onset of puberty, and PQBP1 and SLC35A2 for epilepsy (Grams 2016, Nizon 2015). Furthermore, there are no similar copy number gains of this region in the general populations of the Database of Genomic Variants. Thus, the clinical significance of this copy number variant (CNV) is pathogenic. References: Grams et al., Am J Med Genet A. 2016 Apr;170A(4):967-77. PMID: 26692240. Nizon et al., Am J Med Genet A. 2015 Jan;167A(1):111-22. PMID: 25425167.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 26, 2023

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