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GRCh37/hg19 1q21.1-21.2(chr1:146043714-147819815)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 7, 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:
RCV003484037.1

Allele description [Variation Report for GRCh37/hg19 1q21.1-21.2(chr1:146043714-147819815)x3]

GRCh37/hg19 1q21.1-21.2(chr1:146043714-147819815)x3

Genes:
  • BCL9:BCL9 transcription coactivator [Gene - OMIM - HGNC]
  • GPR89B:G protein-coupled receptor 89B [Gene - OMIM - HGNC]
  • NBPF11:NBPF member 11 [Gene - OMIM - HGNC]
  • NBPF12:NBPF member 12 [Gene - OMIM - HGNC]
  • ACP6:acid phosphatase 6, lysophosphatidic [Gene - OMIM - HGNC]
  • CHD1L:chromodomain helicase DNA binding protein 1 like [Gene - OMIM - HGNC]
  • FMO5:flavin containing dimethylaniline monoxygenase 5 [Gene - OMIM - HGNC]
  • GJA5:gap junction protein alpha 5 [Gene - OMIM - HGNC]
  • GJA8:gap junction protein alpha 8 [Gene - OMIM - HGNC]
  • PRKAB2:protein kinase AMP-activated non-catalytic subunit beta 2 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
1q21.1-21.2
Genomic location:
Chr1: 146043714 - 147819815 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 1q21.1-21.2(chr1:146043714-147819815)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
    SCV004230809Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Sep 7, 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.

    PubMed [citation]
    PMID:
    31690835
    PMCID:
    PMC7313390

    Details of each submission

    From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004230809.1

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

    Description

    This gain of 1q21.1q21.2 is associated with chromosome 1q21.1 duplication syndrome (OMIM 612475). De novo and inherited duplications of the 1q21.1 region have been associated with a broad range of features, and duplications are significantly enriched in schizophrenia and tetralogy of Fallot (TOF) cases compared with controls (Mefford 2008, Brunetti-Pierri 2008, Soemedi 2012, Dolcetti 2013, Digilio 2013, Bernier 2016, Wang 2017). Incomplete penetrance and variable expressivity have been demonstrated for duplication of this region. 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. References: Bernier et al., Genet Med. 2016 Apr;18(4):341-9. PMID: 26066539 Brunetti-Pierri et al., Nat Genet. 2008 Dec;40(12):1466-71. PMID: 19029900 Digilio et al., Eur J Med Genet. 2013 Mar;56(3):144-9. PMID: 23270675 Dolcetti et al., Genet Med. 2013 Apr;15(4):282-9. PMID: 23018752 Mefford et al., N Engl J Med. 2008 Oct 16;359(16):1685-99. PMID: 18784092 Soemedi et al., Hum Mol Genet. 2012 Apr 1;21(7):1513-20. PMID: 22199024 Wang et al., J Gene Med. 2017 Apr;19(4):e2948. PMID: 28220983

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

    Last Updated: Feb 4, 2024