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GRCh37/hg19 Xq21.1-24(chrX:77212972-118576590)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 9, 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:
RCV003485304.2

Allele description [Variation Report for GRCh37/hg19 Xq21.1-24(chrX:77212972-118576590)x3]

GRCh37/hg19 Xq21.1-24(chrX:77212972-118576590)x3

Genes:
  • HTR2C:5-hydroxytryptamine receptor 2C [Gene - OMIM - HGNC]
  • ARL13A:ADP ribosylation factor like GTPase 13A [Gene - HGNC]
  • ALG13:ALG13 UDP-N-acetylglucosaminyltransferase subunit [Gene - OMIM - HGNC]
  • AMMECR1:AMMECR nuclear protein 1 [Gene - OMIM - HGNC]
  • ARMCX3-AS1:ARMCX3 antisense RNA 1 [Gene - HGNC]
  • ARMCX5-GPRASP2:ARMCX5-GPRASP2 readthrough [Gene - HGNC]
  • ATP7A:ATPase copper transporting alpha [Gene - OMIM - HGNC]
  • BTK:Bruton tyrosine kinase [Gene - OMIM - HGNC]
  • CHM:CHM Rab escort protein [Gene - OMIM - HGNC]
  • CPXCR1:CPX chromosome region candidate 1 [Gene - OMIM - HGNC]
  • DANT2:DXZ4 associated non-coding transcript 2, distal [Gene - OMIM - HGNC]
  • ESX1:ESX homeobox 1 [Gene - OMIM - HGNC]
  • FRMPD3:FERM and PDZ domain containing 3 [Gene - OMIM - HGNC]
  • GPR174:G protein-coupled receptor 174 [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]
  • KIAA1210:KIAA1210 [Gene - OMIM - HGNC]
  • LHFPL1:LHFPL tetraspan subfamily member 1 [Gene - OMIM - HGNC]
  • LONRF3:LON peptidase N-terminal domain and ring finger 3 [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]
  • P2RY10:P2Y receptor family member 10 [Gene - OMIM - HGNC]
  • POF1B:POF1B actin binding protein [Gene - OMIM - HGNC]
  • POU3F4:POU class 3 homeobox 4 [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]
  • RBMXL3:RBMX like 3 [Gene - 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]
  • SH3BGRL:SH3 domain binding glutamate rich protein like [Gene - OMIM - HGNC]
  • TBX22:T-box transcription factor 22 [Gene - OMIM - HGNC]
  • TAF7L:TATA-box binding protein associated factor 7 like [Gene - OMIM - HGNC]
  • TAF9B:TATA-box binding protein associated factor 9b [Gene - OMIM - HGNC]
  • TBC1D8B:TBC1 domain family member 8B [Gene - OMIM - HGNC]
  • TGIF2LX:TGFB induced factor homeobox 2 like X-linked [Gene - OMIM - HGNC]
  • TRPC5OS:TRPC5 opposite strand [Gene - HGNC]
  • TSC22D3:TSC22 domain family member 3 [Gene - OMIM - HGNC]
  • VSIG1:V-set and immunoglobulin domain containing 1 [Gene - OMIM - HGNC]
  • WDR44:WD repeat domain 44 [Gene - OMIM - HGNC]
  • XKRX:XK related X-linked [Gene - OMIM - HGNC]
  • ACSL4:acyl-CoA synthetase long chain family member 4 [Gene - OMIM - HGNC]
  • AMOT:angiomotin [Gene - OMIM - HGNC]
  • AGTR2:angiotensin II receptor type 2 [Gene - OMIM - HGNC]
  • APOOL:apolipoprotein O like [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]
  • ATG4A:autophagy related 4A cysteine peptidase [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]
  • BRWD3:bromodomain and WD repeat domain containing 3 [Gene - OMIM - HGNC]
  • CAPN6:calpain 6 [Gene - OMIM - HGNC]
  • CT83:cancer/testis antigen 83 [Gene - OMIM - HGNC]
  • CENPI:centromere protein I [Gene - OMIM - HGNC]
  • CHRDL1:chordin like 1 [Gene - OMIM - HGNC]
  • CLDN2:claudin 2 [Gene - OMIM - HGNC]
  • CSTF2:cleavage stimulation factor subunit 2 [Gene - OMIM - HGNC]
  • COL4A5:collagen type IV alpha 5 chain [Gene - OMIM - HGNC]
  • COL4A6:collagen type IV alpha 6 chain [Gene - OMIM - HGNC]
  • CYLC1:cylicin 1 [Gene - OMIM - HGNC]
  • CYSLTR1:cysteinyl leukotriene receptor 1 [Gene - OMIM - HGNC]
  • DACH2:dachshund family transcription factor 2 [Gene - OMIM - HGNC]
  • DOCK11:dedicator of cytokinesis 11 [Gene - OMIM - HGNC]
  • DIAPH2:diaphanous related formin 2 [Gene - OMIM - HGNC]
  • DCX:doublecortin [Gene - OMIM - HGNC]
  • DNAAF6:dynein axonemal assembly factor 6 [Gene - OMIM - HGNC]
  • DRP2:dystrophin related protein 2 [Gene - OMIM - HGNC]
  • FAM133A:family with sequence similarity 133 member A [Gene - HGNC]
  • FAM199X:family with sequence similarity 199, X-linked [Gene - HGNC]
  • GLA:galactosidase alpha [Gene - OMIM - HGNC]
  • GUCY2F:guanylate cyclase 2F, retinal [Gene - OMIM - HGNC]
  • HNRNPH2:heterogeneous nuclear ribonucleoprotein H2 [Gene - OMIM - HGNC]
  • HMGN5:high mobility group nucleosome binding domain 5 [Gene - OMIM - HGNC]
  • HDX:highly divergent homeobox [Gene - OMIM - HGNC]
  • IRS4:insulin receptor substrate 4 [Gene - OMIM - HGNC]
  • ITM2A:integral membrane protein 2A [Gene - OMIM - HGNC]
  • IL1RAPL2:interleukin 1 receptor accessory protein like 2 [Gene - OMIM - HGNC]
  • IL13RA1:interleukin 13 receptor subunit alpha 1 [Gene - OMIM - HGNC]
  • IL13RA2:interleukin 13 receptor subunit alpha 2 [Gene - OMIM - HGNC]
  • KLHL13:kelch like family member 13 [Gene - OMIM - HGNC]
  • KLHL4:kelch like family member 4 [Gene - OMIM - HGNC]
  • LRCH2:leucine rich repeats and calponin homology domain containing 2 [Gene - HGNC]
  • LUZP4:leucine zipper protein 4 [Gene - OMIM - HGNC]
  • LPAR4:lysophosphatidic acid receptor 4 [Gene - OMIM - HGNC]
  • MIR448:microRNA 448 [Gene - OMIM - HGNC]
  • MID2:midline 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]
  • NXT2:nuclear transport factor 2 like export factor 2 [Gene - OMIM - HGNC]
  • NUP62CL:nucleoporin 62 C-terminal like [Gene - HGNC]
  • NAP1L3:nucleosome assembly protein 1 like 3 [Gene - OMIM - HGNC]
  • PAK3:p21 (RAC1) activated kinase 3 [Gene - OMIM - HGNC]
  • PGK1:phosphoglycerate kinase 1 [Gene - OMIM - HGNC]
  • PGAM4:phosphoglycerate mutase family member 4 [Gene - OMIM - HGNC]
  • PRPS1:phosphoribosyl pyrophosphate synthetase 1 [Gene - OMIM - HGNC]
  • PLS3:plastin 3 [Gene - OMIM - HGNC]
  • PABPC5:poly(A) binding protein cytoplasmic 5 [Gene - OMIM - HGNC]
  • KCNE5:potassium voltage-gated channel subfamily E regulatory subunit 5 [Gene - OMIM - HGNC]
  • PGRMC1:progesterone receptor membrane component 1 [Gene - OMIM - HGNC]
  • PSMD10:proteasome 26S subunit, non-ATPase 10 [Gene - OMIM - HGNC]
  • PLP1:proteolipid protein 1 [Gene - OMIM - HGNC]
  • PCDH11X:protocadherin 11 X-linked [Gene - OMIM - HGNC]
  • PCDH19:protocadherin 19 [Gene - OMIM - HGNC]
  • RPA4:replication protein A4 [Gene - OMIM - HGNC]
  • RTL3:retrotransposon Gag like 3 [Gene - HGNC]
  • RTL4:retrotransposon Gag like 4 [Gene - HGNC]
  • RTL9:retrotransposon Gag like 9 [Gene - OMIM - HGNC]
  • RPL36A:ribosomal protein L36a [Gene - OMIM - HGNC]
  • RPS6KA6:ribosomal protein S6 kinase A6 [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]
  • SLC25A43:solute carrier family 25 member 43 [Gene - OMIM - HGNC]
  • SLC25A53:solute carrier family 25 member 53 [Gene - OMIM - HGNC]
  • SLC6A14:solute carrier family 6 member 14 [Gene - OMIM - HGNC]
  • SATL1:spermidine/spermine N1-acetyl transferase like 1 [Gene - 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]
  • TENT5D:terminal nucleotidyltransferase 5D [Gene - OMIM - HGNC]
  • TEX13A:testis expressed 13A [Gene - OMIM - HGNC]
  • TEX13B:testis expressed 13B [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]
  • TRPC5:transient receptor potential cation channel subfamily C member 5 [Gene - OMIM - HGNC]
  • TIMM8A:translocase of inner mitochondrial membrane 8A [Gene - OMIM - HGNC]
  • TMEM164:transmembrane protein 164 [Gene - HGNC]
  • TMEM31:transmembrane protein 31 [Gene - OMIM - HGNC]
  • TMEM35A:transmembrane protein 35A [Gene - HGNC]
  • ZCCHC12:zinc finger CCHC-type containing 12 [Gene - OMIM - HGNC]
  • ZCCHC18:zinc finger CCHC-type containing 18 [Gene - HGNC]
  • ZMAT1:zinc finger matrin-type 1 [Gene - OMIM - HGNC]
  • ZNF711:zinc finger protein 711 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
Xq21.1-24
Genomic location:
ChrX: 77212972 - 118576590 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 Xq21.1-24(chrX:77212972-118576590)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
    SCV004231230Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Jul 9, 2022)     		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, SCV004231230.1

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

    Description

    The copy number gain of Xq21.1q24 involves numerous protein-coding genes, including PLP1 (OMIM 300401, Chen 2011, Parissone 2020). Duplication of PLP1 is associated with Pelizaeus-Merzbacher disease (PMD; OMIM 312080) and spastic paraplegia 2 (SPG2; OMIM 312920). Duplication size along with genomic content can be an important factor for penetrance of the PMD phenotype in females (Carvalho 2012, Wolf 1999, Masliah-Planchon 2015). Based on current medical literature and gene content, the classification of this gain is pathogenic. References:_x000D__x000D_ Carvalho et al., Clin Genet. 2012 Jun;81(6):532-41. PMID: 21623770_x000D__x000D_ Chen et al., Taiwan J Obstet Gynecol. 2011 Sep;50(3):339-44. PMID: 22030050_x000D__x000D_ Masliah-Planchon et al., BMC Med Genet. 2015 Sep 2;16:77. PMID: 26329556_x000D__x000D_ Parissone et al., Int J Pediatr Endocrinol. 2020;2020:1. PMID: 31938033_x000D__x000D_ Wolf et al., PLP1 Disorders. 1999 Jun [Updated 2019 Dec]. In: Adam et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2022. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1182/

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

    Last Updated: Jun 23, 2024