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GRCh37/hg19 Xq21.33-22.3(chrX:96349060-106950847)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 2, 2023
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:
RCV003485308.1

Allele description [Variation Report for GRCh37/hg19 Xq21.33-22.3(chrX:96349060-106950847)x3]

GRCh37/hg19 Xq21.33-22.3(chrX:96349060-106950847)x3

Genes:
  • ARL13A:ADP ribosylation factor like GTPase 13A [Gene - HGNC]
  • ARMCX3-AS1:ARMCX3 antisense RNA 1 [Gene - HGNC]
  • ARMCX5-GPRASP2:ARMCX5-GPRASP2 readthrough [Gene - HGNC]
  • BTK:Bruton tyrosine kinase [Gene - OMIM - HGNC]
  • ESX1:ESX homeobox 1 [Gene - OMIM - HGNC]
  • FRMPD3:FERM and PDZ domain containing 3 [Gene - OMIM - HGNC]
  • GPRASP1:G protein-coupled receptor associated sorting protein 1 [Gene - OMIM - HGNC]
  • GPRASP2:G protein-coupled receptor associated sorting protein 2 [Gene - OMIM - HGNC]
  • GPRASP3:G protein-coupled receptor associated sorting protein family member 3 [Gene - OMIM - HGNC]
  • H2BW1:H2B.W histone 1 [Gene - OMIM - HGNC]
  • H2BW2:H2B.W histone 2 [Gene - HGNC]
  • MORC4:MORC family CW-type zinc finger 4 [Gene - OMIM - HGNC]
  • NOX1:NADPH oxidase 1 [Gene - OMIM - HGNC]
  • NRK:Nik related kinase [Gene - OMIM - HGNC]
  • PWWP3B:PWWP domain containing 3B [Gene - HGNC]
  • RAB40AL:RAB40A like [Gene - OMIM - HGNC]
  • RAB40A:RAB40A, member RAS oncogene family [Gene - OMIM - HGNC]
  • RAB9B:RAB9B, member RAS oncogene family [Gene - OMIM - HGNC]
  • RBM41:RNA binding motif protein 41 [Gene - HGNC]
  • RADX:RPA1 related single stranded DNA binding protein, X-linked [Gene - HGNC]
  • RPL36A-HNRNPH2:RPL36A-HNRNPH2 readthrough [Gene - HGNC]
  • TAF7L:TATA-box binding protein associated factor 7 like [Gene - OMIM - HGNC]
  • TBC1D8B:TBC1 domain family member 8B [Gene - OMIM - HGNC]
  • XKRX:XK related X-linked [Gene - OMIM - HGNC]
  • ARMCX1:armadillo repeat containing X-linked 1 [Gene - OMIM - HGNC]
  • ARMCX2:armadillo repeat containing X-linked 2 [Gene - OMIM - HGNC]
  • ARMCX3:armadillo repeat containing X-linked 3 [Gene - OMIM - HGNC]
  • ARMCX4:armadillo repeat containing X-linked 4 [Gene - OMIM - HGNC]
  • ARMCX5:armadillo repeat containing X-linked 5 [Gene - OMIM - HGNC]
  • ARMCX6:armadillo repeat containing X-linked 6 [Gene - OMIM - HGNC]
  • BEX1:brain expressed X-linked 1 [Gene - OMIM - HGNC]
  • BEX2:brain expressed X-linked 2 [Gene - OMIM - HGNC]
  • BEX3:brain expressed X-linked 3 [Gene - OMIM - HGNC]
  • BEX4:brain expressed X-linked 4 [Gene - OMIM - HGNC]
  • BEX5:brain expressed X-linked 5 [Gene - OMIM - HGNC]
  • CENPI:centromere protein I [Gene - OMIM - HGNC]
  • CLDN2:claudin 2 [Gene - OMIM - HGNC]
  • CSTF2:cleavage stimulation factor subunit 2 [Gene - OMIM - HGNC]
  • DIAPH2:diaphanous related formin 2 [Gene - OMIM - HGNC]
  • DNAAF6:dynein axonemal assembly factor 6 [Gene - OMIM - HGNC]
  • DRP2:dystrophin related protein 2 [Gene - OMIM - HGNC]
  • FAM199X:family with sequence similarity 199, X-linked [Gene - HGNC]
  • GLA:galactosidase alpha [Gene - OMIM - HGNC]
  • HNRNPH2:heterogeneous nuclear ribonucleoprotein H2 [Gene - OMIM - HGNC]
  • IL1RAPL2:interleukin 1 receptor accessory protein like 2 [Gene - OMIM - HGNC]
  • MORF4L2:mortality factor 4 like 2 [Gene - OMIM - HGNC]
  • NXF2:nuclear RNA export factor 2 [Gene - OMIM - HGNC]
  • NXF2B:nuclear RNA export factor 2B [Gene - HGNC]
  • NXF3:nuclear RNA export factor 3 [Gene - OMIM - HGNC]
  • NXF5:nuclear RNA export factor 5 [Gene - OMIM - HGNC]
  • NUP62CL:nucleoporin 62 C-terminal like [Gene - HGNC]
  • PRPS1:phosphoribosyl pyrophosphate synthetase 1 [Gene - OMIM - HGNC]
  • PLP1:proteolipid protein 1 [Gene - OMIM - HGNC]
  • PCDH19:protocadherin 19 [Gene - OMIM - HGNC]
  • RPL36A:ribosomal protein L36a [Gene - OMIM - HGNC]
  • RNF128:ring finger protein 128 [Gene - OMIM - HGNC]
  • RIPPLY1:ripply transcriptional repressor 1 [Gene - OMIM - HGNC]
  • SERPINA7:serpin family A member 7 [Gene - OMIM - HGNC]
  • SLC25A53:solute carrier family 25 member 53 [Gene - OMIM - HGNC]
  • SRPX2:sushi repeat containing protein X-linked 2 [Gene - OMIM - HGNC]
  • SYTL4:synaptotagmin like 4 [Gene - OMIM - HGNC]
  • TCP11X2:t-complex 11 family, X-linked 2 [Gene - HGNC]
  • TRMT2B:tRNA methyltransferase 2 homolog B [Gene - HGNC]
  • TNMD:tenomodulin [Gene - OMIM - HGNC]
  • TEX13A:testis expressed 13A [Gene - OMIM - HGNC]
  • TSPAN6:tetraspanin 6 [Gene - OMIM - HGNC]
  • TMSB15A:thymosin beta 15A [Gene - OMIM - HGNC]
  • TMSB15B:thymosin beta 15B [Gene - OMIM - HGNC]
  • TCEAL1:transcription elongation factor A like 1 [Gene - OMIM - HGNC]
  • TCEAL2:transcription elongation factor A like 2 [Gene - HGNC]
  • TCEAL3:transcription elongation factor A like 3 [Gene - HGNC]
  • TCEAL4:transcription elongation factor A like 4 [Gene - HGNC]
  • TCEAL5:transcription elongation factor A like 5 [Gene - HGNC]
  • TCEAL6:transcription elongation factor A like 6 [Gene - HGNC]
  • TCEAL7:transcription elongation factor A like 7 [Gene - OMIM - HGNC]
  • TCEAL8:transcription elongation factor A like 8 [Gene - HGNC]
  • TCEAL9:transcription elongation factor A like 9 [Gene - HGNC]
  • TIMM8A:translocase of inner mitochondrial membrane 8A [Gene - OMIM - HGNC]
  • TMEM31:transmembrane protein 31 [Gene - OMIM - HGNC]
  • TMEM35A:transmembrane protein 35A [Gene - HGNC]
  • ZCCHC18:zinc finger CCHC-type containing 18 [Gene - HGNC]
  • ZMAT1:zinc finger matrin-type 1 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
Xq21.33-22.3
Genomic location:
ChrX: 96349060 - 106950847 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 Xq21.33-22.3(chrX:96349060-106950847)x3
HGVS:

    Condition(s)

    Synonyms:
    none provided
    Identifiers:
    MedGen: C3661900

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV004231234Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Feb 2, 2023)     		unknownclinical testing

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

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    not providedunknownunknownnot providednot providednot providednot providednot providedclinical 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, SCV004231234.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedclinical testing PubMed (1)

    Description

    This gain contains numerous protein-coding genes, including multiple genes associated with X-linked disorders. Haploinsufficiency and triplosensitivity of PLP1 is associated with Pelizaeus-Merzbacher disease (PMD; OMIM 312080, Rehm 2015, Bertoli-Avella 2021). Duplications involving Xq22 have been identified in females with a milder phenotype (Carvalho 2012, Masliah-Planchon 2015, Willemsen 2012). There are no similar copy number gains of this region in the general populations of the Database of Genomic Variants. Thus, based on current medical literature and gene content, this copy number variant (CNV) is classified as pathogenic, though clinical presentation in a female is likely dependent upon X-inactivation status. References: Bertoli-Avella et al., Eur J Hum Genet. 2021 Jan;29(1):141-153. PMID: 32860008 Carvalho et al., Clin Genet. 2012 Jun;81(6):532-41. PMID: 21623770 Masliah-Planchon et al., BMC Med Genet. 2015 Sep 2;16:77. PMID: 26329556 Rehm et al., N Engl J Med. 2015 Jun 4;372(23):2235-42. PMID: 26014595 Willemsen et al., Eur J Med Genet. 2012 Nov;55(11):586-98. PMID: 22796527

    #SampleMethodObservation
    OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
    1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

    Last Updated: Feb 4, 2024