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GRCh37/hg19 15q11.2-13.3(chr15:22770422-32915593)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 20, 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:
RCV003485057.1

Allele description [Variation Report for GRCh37/hg19 15q11.2-13.3(chr15:22770422-32915593)x3]

GRCh37/hg19 15q11.2-13.3(chr15:22770422-32915593)x3

Genes:
  • ATP10A:ATPase phospholipid transporting 10A (putative) [Gene - OMIM - HGNC]
  • CHRFAM7A:CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion [Gene - OMIM - HGNC]
  • FAN1:FANCD2 and FANCI associated nuclease 1 [Gene - OMIM - HGNC]
  • HERC2:HECT and RLD domain containing E3 ubiquitin protein ligase 2 [Gene - OMIM - HGNC]
  • KLF13:KLF transcription factor 13 [Gene - OMIM - HGNC]
  • MAGEL2:MAGE family member L2 [Gene - OMIM - HGNC]
  • NIPA1:NIPA magnesium transporter 1 [Gene - OMIM - HGNC]
  • NIPA2:NIPA magnesium transporter 2 [Gene - OMIM - HGNC]
  • NSMCE3:NSE3 homolog, SMC5-SMC6 complex component [Gene - OMIM - HGNC]
  • OCA2:OCA2 melanosomal transmembrane protein [Gene - OMIM - HGNC]
  • OTUD7A:OTU deubiquitinase 7A [Gene - OMIM - HGNC]
  • PWAR1:Prader Willi/Angelman region RNA 1 [Gene - OMIM - HGNC]
  • PWAR4:Prader Willi/Angelman region RNA 4 [Gene - HGNC]
  • PWAR5:Prader Willi/Angelman region RNA 5 [Gene - OMIM - HGNC]
  • PWAR6:Prader Willi/Angelman region RNA 6 [Gene - HGNC]
  • PWARSN:Prader Willi/Angelman region RNA, SNRPN neighbor [Gene - HGNC]
  • PWRN1:Prader-Willi region non-protein coding RNA 1 [Gene - OMIM - HGNC]
  • PWRN2:Prader-Willi region non-protein coding RNA 2 [Gene - OMIM - HGNC]
  • ARHGAP11A:Rho GTPase activating protein 11A [Gene - OMIM - HGNC]
  • ARHGAP11B:Rho GTPase activating protein 11B [Gene - OMIM - HGNC]
  • SNURF:SNRPN upstream open reading frame [Gene - HGNC]
  • APBA2:amyloid beta precursor protein binding family A member 2 [Gene - OMIM - HGNC]
  • CHRNA7:cholinergic receptor nicotinic alpha 7 subunit [Gene - OMIM - HGNC]
  • CYFIP1:cytoplasmic FMR1 interacting protein 1 [Gene - OMIM - HGNC]
  • ENTREP2:endosomal transmembrane epsin interactor 2 [Gene - OMIM - HGNC]
  • GABRA5:gamma-aminobutyric acid type A receptor subunit alpha5 [Gene - OMIM - HGNC]
  • GABRB3:gamma-aminobutyric acid type A receptor subunit beta3 [Gene - OMIM - HGNC]
  • GABRG3:gamma-aminobutyric acid type A receptor subunit gamma3 [Gene - OMIM - HGNC]
  • GOLGA6L2:golgin A6 family like 2 [Gene - HGNC]
  • GOLGA8H:golgin A8 family member H [Gene - HGNC]
  • GOLGA8J:golgin A8 family member J [Gene - HGNC]
  • GOLGA8M:golgin A8 family member M [Gene - HGNC]
  • GOLGA8N:golgin A8 family member N [Gene - HGNC]
  • GOLGA8O:golgin A8 family member O [Gene - HGNC]
  • IPW:imprinted in Prader-Willi syndrome [Gene - OMIM - HGNC]
  • MKRN3:makorin ring finger protein 3 [Gene - OMIM - HGNC]
  • MIR211:microRNA 211 [Gene - OMIM - HGNC]
  • MTMR10:myotubularin related protein 10 [Gene - HGNC]
  • NDN:necdin, MAGE family member [Gene - OMIM - HGNC]
  • NPAP1:nuclear pore associated protein 1 [Gene - OMIM - HGNC]
  • SNRPN:small nuclear ribonucleoprotein polypeptide N [Gene - OMIM - HGNC]
  • SNORD115-1:small nucleolar RNA, C/D box 115-1 [Gene - OMIM - HGNC]
  • SNORD116-1:small nucleolar RNA, C/D box 116-1 [Gene - OMIM - HGNC]
  • TJP1:tight junction protein 1 [Gene - OMIM - HGNC]
  • TRPM1:transient receptor potential cation channel subfamily M member 1 [Gene - OMIM - HGNC]
  • TUBGCP5:tubulin gamma complex component 5 [Gene - OMIM - HGNC]
  • UBE3A:ubiquitin protein ligase E3A [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
15q11.2-13.3
Genomic location:
Chr15: 22770422 - 32915593 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 15q11.2-13.3(chr15:22770422-32915593)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
    SCV004230983Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Jun 20, 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, SCV004230983.1

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

    Description

    This copy number gain overlaps the Prader Willi/Angelman syndrome (PWS/AS) critical region and the interval (BP1-BP3) associated with recurrent 15q11q13 duplication syndrome (OMIM 608636). Clinical features associated with 15q11-q13 duplication syndrome (OMIM 608636) can vary between and within families (Urraca 2013, Marini 2013, Song 2022, Lusk 2016). Therefore, this copy number variant is classified as pathogenic. References: Lusk et al., GeneReviews [Internet]. Seattle (WA): University of Washington, Seattle; 1993. 2016 Jun 16 [updated 2021 Jul 15]. PMID: 27308687 Marini et al. Am J Med Genet A. 2013;161A(6):1459-64. PMID: 23633446 Urraca et al. Autism Res. 2013;6(4):268-79 PMID: 23495136

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

    Last Updated: Feb 4, 2024