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GRCh37/hg19 7q36.1(chr7:149332630-151498689)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 20, 2021
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:
RCV002472413.1

Allele description [Variation Report for GRCh37/hg19 7q36.1(chr7:149332630-151498689)x1]

GRCh37/hg19 7q36.1(chr7:149332630-151498689)x1

Genes:
  • ABCB8:ATP binding cassette subfamily B member 8 [Gene - OMIM - HGNC]
  • ABCF2:ATP binding cassette subfamily F member 2 [Gene - OMIM - HGNC]
  • ATP6V0E2:ATPase H+ transporting V0 subunit e2 [Gene - OMIM - HGNC]
  • AGAP3:ArfGAP with GTPase domain, ankyrin repeat and PH domain 3 [Gene - OMIM - HGNC]
  • FASTK:Fas activated serine/threonine kinase [Gene - OMIM - HGNC]
  • GIMAP1:GTPase, IMAP family member 1 [Gene - OMIM - HGNC]
  • GIMAP2:GTPase, IMAP family member 2 [Gene - OMIM - HGNC]
  • GIMAP4:GTPase, IMAP family member 4 [Gene - OMIM - HGNC]
  • GIMAP5:GTPase, IMAP family member 5 [Gene - OMIM - HGNC]
  • GIMAP6:GTPase, IMAP family member 6 [Gene - OMIM - HGNC]
  • GIMAP7:GTPase, IMAP family member 7 [Gene - OMIM - HGNC]
  • GIMAP8:GTPase, IMAP family member 8 [Gene - OMIM - HGNC]
  • KRBA1:KRAB-A domain containing 1 [Gene - HGNC]
  • RHEB:Ras homolog, mTORC1 binding [Gene - OMIM - HGNC]
  • SMARCD3:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 [Gene - OMIM - HGNC]
  • WDR86:WD repeat domain 86 [Gene - HGNC]
  • ZBED6CL:ZBED6 C-terminal like [Gene - OMIM - HGNC]
  • ASIC3:acid sensing ion channel subunit 3 [Gene - OMIM - HGNC]
  • ACTR3C:actin related protein 3C [Gene - HGNC]
  • AOC1:amine oxidase copper containing 1 [Gene - OMIM - HGNC]
  • ASB10:ankyrin repeat and SOCS box containing 10 [Gene - OMIM - HGNC]
  • ATG9B:autophagy related 9B [Gene - OMIM - HGNC]
  • CHPF2:chondroitin polymerizing factor 2 [Gene - OMIM - HGNC]
  • CRYGN:crystallin gamma N [Gene - OMIM - HGNC]
  • CDK5:cyclin dependent kinase 5 [Gene - OMIM - HGNC]
  • GBX1:gastrulation brain homeobox 1 [Gene - OMIM - HGNC]
  • LRRC61:leucine rich repeat containing 61 [Gene - HGNC]
  • MIR671:microRNA 671 [Gene - OMIM - HGNC]
  • NUB1:negative regulator of ubiquitin like proteins 1 [Gene - OMIM - HGNC]
  • NOS3:nitric oxide synthase 3 [Gene - OMIM - HGNC]
  • KCNH2:potassium voltage-gated channel subfamily H member 2 [Gene - OMIM - HGNC]
  • PRKAG2:protein kinase AMP-activated non-catalytic subunit gamma 2 [Gene - OMIM - HGNC]
  • REPIN1:replication initiator 1 [Gene - OMIM - HGNC]
  • RARRES2:retinoic acid receptor responder 2 [Gene - OMIM - HGNC]
  • SLC4A2:solute carrier family 4 member 2 [Gene - OMIM - HGNC]
  • TMUB1:transmembrane and ubiquitin like domain containing 1 [Gene - OMIM - HGNC]
  • TMEM176A:transmembrane protein 176A [Gene - OMIM - HGNC]
  • TMEM176B:transmembrane protein 176B [Gene - OMIM - HGNC]
  • LOC100134040:uncharacterized LOC100134040 [Gene - OMIM]
  • ZNF467:zinc finger protein 467 [Gene - OMIM - HGNC]
  • ZNF775:zinc finger protein 775 [Gene - HGNC]
  • ZNF862:zinc finger protein 862 [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
7q36.1
Genomic location:
Chr7: 149332630 - 151498689 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 7q36.1(chr7:149332630-151498689)x1
HGVS:

    Condition(s)

    Synonyms:
    none provided
    Identifiers:
    MedGen: CN517202

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV002772281Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Dec 20, 2021)     		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, SCV002772281.1

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

    Description

    The copy number loss of 7q36.1 involves numerous protein-coding genes, including KCNH2 (OMIM 152427) and multiple exons (NM_016203.4) of the 3' portion of PRKAG2 (OMIM 602743), and is expected to cause phenotypic and/or developmental abnormalities. Hemizygous deletions as well as heterozygous loss-of-function sequence variants of KCNH2 are associated with autosomal dominant long QT syndrome 2 (LQT2; OMIM 613688), which is characterized by polymorphic ventricular arrhythmias which may result in recurrent syncope, seizure, or sudden mortality. Similar sequence variants within KCNH2 have also been associated with short QT syndrome-1 (SQT1; OMIM 609620), which is a cardiac channelopathy associated with a predisposition to atrial fibrillation and sudden cardiac death. Furthermore, heterozygous sequence variants of PRKAG2 are associated with autosomal dominant lethal congenital glycogen storage disease of the heart (OMIM 261740), hypertrophic cardiomyopathy-6 (CMH6; OMIM 600858), and Wolff-Parkinson-White preexcitation syndrome (WPW syndrome) (OMIM 194200) in isolation or in association with cardiac hypertrophy. There are no similar copy number losses of this region in the general populations of the Database of Genomic Variants. Based on the genecontent and size of this copy number variant (CNV), the classification is pathogenic. References Iossifov et al., Nature. 2014 Nov 13;515(7526):216-21. PMID: 25363768. Potocki et al., Am J Hum Genet. 2007 Apr;80(4):633-49. PMID: 17357070. Satterstrom et al., Cell. 2020 Feb 6;180(3):568-584.e23. PMID: 31981491. Turner et al., Am J Hum Genet. 2019 Dec 5;105(6):1274-1285. PMID: 31785789.

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

    Last Updated: Dec 31, 2022