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GRCh37/hg19 7q36.1(chr7:148538593-150967829)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 3, 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:
RCV003482992.1

Allele description [Variation Report for GRCh37/hg19 7q36.1(chr7:148538593-150967829)x1]

GRCh37/hg19 7q36.1(chr7:148538593-150967829)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]
  • RNY1:RNA, Ro60-associated Y1 [Gene - OMIM - HGNC]
  • RNY3:RNA, Ro60-associated Y3 [Gene - OMIM - HGNC]
  • RNY4:RNA, Ro60-associated Y4 [Gene - OMIM - HGNC]
  • RNY5:RNA, Ro60-associated Y5 [Gene - OMIM - HGNC]
  • SMARCD3:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 [Gene - OMIM - 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]
  • CDK5:cyclin dependent kinase 5 [Gene - OMIM - HGNC]
  • EZH2:enhancer of zeste 2 polycomb repressive complex 2 subunit [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]
  • NOS3:nitric oxide synthase 3 [Gene - OMIM - HGNC]
  • KCNH2:potassium voltage-gated channel subfamily H member 2 [Gene - OMIM - HGNC]
  • PDIA4:protein disulfide isomerase family A member 4 [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]
  • ZNF212:zinc finger protein 212 [Gene - OMIM - HGNC]
  • ZNF282:zinc finger protein 282 [Gene - OMIM - HGNC]
  • ZNF398:zinc finger protein 398 [Gene - OMIM - HGNC]
  • ZNF425:zinc finger protein 425 [Gene - OMIM - HGNC]
  • ZNF467:zinc finger protein 467 [Gene - OMIM - HGNC]
  • ZNF746:zinc finger protein 746 [Gene - OMIM - HGNC]
  • ZNF775:zinc finger protein 775 [Gene - HGNC]
  • ZNF777:zinc finger protein 777 [Gene - OMIM - HGNC]
  • ZNF783:zinc finger protein 783 [Gene - HGNC]
  • ZNF786:zinc finger protein 786 [Gene - HGNC]
  • ZNF862:zinc finger protein 862 [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
7q36.1
Genomic location:
Chr7: 148538593 - 150967829 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 7q36.1(chr7:148538593-150967829)x1
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
    SCV004231509Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (May 3, 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, SCV004231509.1

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

    Description

    This loss involves multiple protein-coding genes. Haploinsufficiency of KCNH2 is associated with autosomal dominant long QT syndrome 2 (OMIM 613688, Singer 2021). A heterozygous deletion involving the full EZH2 gene was identified in an individual with some overlapping features of Weaver Syndrome (Suri 2017). There are no similar copy number losses spanning this region in the general populations of the Database of Genomic Variants. Thus, based on gene content and current medical literature, this copy number variant (CNV) is classified as pathogenic. References: Singer et al., Genet Med. 2021 Jan;23(1):86-93. PMID: 32973354 Suri et al., Am J Med Genet A. 2017 Oct;173(10):2731-2735. PMID: 28696078

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

    Last Updated: Feb 4, 2024