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GRCh37/hg19 6p25.3-22.3(chr6:156975-15478095)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:
RCV003484635.1

Allele description [Variation Report for GRCh37/hg19 6p25.3-22.3(chr6:156975-15478095)x3]

GRCh37/hg19 6p25.3-22.3(chr6:156975-15478095)x3

Genes:
  • CD83:CD83 molecule [Gene - OMIM - HGNC]
  • ELOVL2:ELOVL fatty acid elongase 2 [Gene - OMIM - HGNC]
  • GMDS:GDP-mannose 4,6-dehydratase [Gene - OMIM - HGNC]
  • GFOD1:Gfo/Idh/MocA-like oxidoreductase domain containing 1 [Gene - OMIM - HGNC]
  • HIVEP1:HIVEP zinc finger 1 [Gene - OMIM - HGNC]
  • HUS1B:HUS1 checkpoint clamp component B [Gene - OMIM - HGNC]
  • LYRM4:LYR motif containing 4 [Gene - OMIM - HGNC]
  • NQO2:N-ribosyldihydronicotinamide:quinone dehydrogenase 2 [Gene - OMIM - HGNC]
  • PAK1IP1:PAK1 interacting protein 1 [Gene - OMIM - HGNC]
  • PXDC1:PX domain containing 1 [Gene - HGNC]
  • RANBP9:RAN binding protein 9 [Gene - OMIM - HGNC]
  • RIOK1:RIO kinase 1 [Gene - OMIM - HGNC]
  • TBC1D7:TBC1 domain family member 7 [Gene - OMIM - HGNC]
  • WRNIP1:WRN helicase interacting protein 1 [Gene - OMIM - HGNC]
  • ADTRP:androgen dependent TFPI regulating protein [Gene - OMIM - HGNC]
  • BLOC1S5:biogenesis of lysosomal organelles complex 1 subunit 5 [Gene - OMIM - HGNC]
  • BPHL:biphenyl hydrolase like [Gene - OMIM - HGNC]
  • BMP6:bone morphogenetic protein 6 [Gene - OMIM - HGNC]
  • CAGE1:cancer antigen 1 [Gene - OMIM - HGNC]
  • CDYL:chromodomain Y like [Gene - OMIM - HGNC]
  • C6orf201:chromosome 6 open reading frame 201 [Gene - HGNC]
  • C6orf52:chromosome 6 open reading frame 52 [Gene - HGNC]
  • F13A1:coagulation factor XIII A chain [Gene - OMIM - HGNC]
  • DSP:desmoplakin [Gene - OMIM - HGNC]
  • DUSP22:dual specificity phosphatase 22 [Gene - OMIM - HGNC]
  • ERVFRD-1:endogenous retrovirus group FRD member 1, envelope [Gene - OMIM - HGNC]
  • EDN1:endothelin 1 [Gene - OMIM - HGNC]
  • ECI2:enoyl-CoA delta isomerase 2 [Gene - OMIM - HGNC]
  • EEF1E1:eukaryotic translation elongation factor 1 epsilon 1 [Gene - OMIM - HGNC]
  • EXOC2:exocyst complex component 2 [Gene - OMIM - HGNC]
  • FAM217A:family with sequence similarity 217 member A [Gene - HGNC]
  • FAM50B:family with sequence similarity 50 member B [Gene - OMIM - HGNC]
  • FOXC1:forkhead box C1 [Gene - OMIM - HGNC]
  • FOXF2:forkhead box F2 [Gene - OMIM - HGNC]
  • FOXQ1:forkhead box Q1 [Gene - OMIM - HGNC]
  • GCM2:glial cells missing transcription factor 2 [Gene - OMIM - HGNC]
  • GCNT2:glucosaminyl (N-acetyl) transferase 2 (I blood group) [Gene - OMIM - HGNC]
  • HULC:hepatocellular carcinoma up-regulated long non-coding RNA [Gene - OMIM - HGNC]
  • IRF4:interferon regulatory factor 4 [Gene - OMIM - HGNC]
  • JARID2:jumonji and AT-rich interaction domain containing 2 [Gene - OMIM - HGNC]
  • LINC01600:long intergenic non-protein coding RNA 1600 [Gene - HGNC]
  • LY86:lymphocyte antigen 86 [Gene - OMIM - HGNC]
  • MAK:male germ cell associated kinase [Gene - OMIM - HGNC]
  • MCUR1:mitochondrial calcium uniporter regulator 1 [Gene - OMIM - HGNC]
  • MYLK4:myosin light chain kinase family member 4 [Gene - HGNC]
  • NEDD9:neural precursor cell expressed, developmentally down-regulated 9 [Gene - OMIM - HGNC]
  • NRN1:neuritin 1 [Gene - OMIM - HGNC]
  • NOL7:nucleolar protein 7 [Gene - OMIM - HGNC]
  • OFCC1:orofacial cleft 1 candidate 1 [Gene - OMIM - HGNC]
  • FARS2:phenylalanyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
  • PHACTR1:phosphatase and actin regulator 1 [Gene - OMIM - HGNC]
  • PRP4K:pre-mRNA processing factor kinase PRP4K [Gene - OMIM - HGNC]
  • PSMG4:proteasome assembly chaperone 4 [Gene - OMIM - HGNC]
  • PPP1R3G:protein phosphatase 1 regulatory subunit 3G [Gene - OMIM - HGNC]
  • RREB1:ras responsive element binding protein 1 [Gene - OMIM - HGNC]
  • RIPK1:receptor interacting serine/threonine kinase 1 [Gene - OMIM - HGNC]
  • RPP40:ribonuclease P/MRP subunit p40 [Gene - OMIM - HGNC]
  • RNF182:ring finger protein 182 [Gene - HGNC]
  • SERPINB1:serpin family B member 1 [Gene - OMIM - HGNC]
  • SERPINB6:serpin family B member 6 [Gene - OMIM - HGNC]
  • SERPINB9:serpin family B member 9 [Gene - OMIM - HGNC]
  • SSR1:signal sequence receptor subunit 1 [Gene - OMIM - HGNC]
  • SIRT5:sirtuin 5 [Gene - OMIM - HGNC]
  • SMIM13:small integral membrane protein 13 [Gene - HGNC]
  • SNRNP48:small nuclear ribonucleoprotein U11/U12 subunit 48 [Gene - HGNC]
  • SLC22A23:solute carrier family 22 member 23 [Gene - OMIM - HGNC]
  • SLC35B3:solute carrier family 35 member B3 [Gene - OMIM - HGNC]
  • SYCP2L:synaptonemal complex protein 2 like [Gene - OMIM - HGNC]
  • TFAP2A:transcription factor AP-2 alpha [Gene - OMIM - HGNC]
  • TMEM14B:transmembrane protein 14B [Gene - OMIM - HGNC]
  • TMEM14C:transmembrane protein 14C [Gene - OMIM - HGNC]
  • TMEM170B:transmembrane protein 170B [Gene - HGNC]
  • TUBB2A:tubulin beta 2A class IIa [Gene - OMIM - HGNC]
  • TUBB2B:tubulin beta 2B class IIb [Gene - OMIM - HGNC]
  • KU-MEL-3:uncharacterized LOC497048 [Gene]
Variant type:
copy number gain
Cytogenetic location:
6p25.3-22.3
Genomic location:
Chr6: 156975 - 15478095 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 6p25.3-22.3(chr6:156975-15478095)x3
HGVS:

    Condition(s)

    Synonyms:
    none provided
    Identifiers:
    MedGen: C3661900

    Recent activity

    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV004230496Quest 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.

    PubMed [citation]
    PMID:
    31690835
    PMCID:
    PMC7313390

    Details of each submission

    From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004230496.1

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

    Description

    The copy number gain of 6p25.3p22.3 is associated with 6p partial trisomy. Phenotypes associated with copy number gains of this region are variable and may include seizures, autism, brain abnormalities, hearing loss, ocular defects including Axenfeld-Rieger syndrome, susceptibility to pulmonary infections, and other clinical issues (Castiglione 2013, Souzeau 2017, Peterman 2020). Thus, based on current medical literature and gene content, the classification of this gain is pathogenic. _x000D__x000D_ References_x000D__x000D_ Castiglione et al., Cytogenet Genome Res. 2013;141(4):243-59. PMID: 23942271_x000D__x000D_ Souzeau et al., Eur J Hum Genet. 2017 Jun;25(7):839-847. PMID: 28513611_x000D__x000D_ Peterman et al., Case Rep Genet. 2020 Aug 31;2020:8857628. PMID: 32934853_x000D__x000D_

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

    Last Updated: Feb 4, 2024