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GRCh37/hg19 6p25.3(chr6:647204-1716710)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 20, 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:
RCV003485501.1

Allele description [Variation Report for GRCh37/hg19 6p25.3(chr6:647204-1716710)x1]

GRCh37/hg19 6p25.3(chr6:647204-1716710)x1

Genes:
Variant type:
copy number loss
Cytogenetic location:
6p25.3
Genomic location:
Chr6: 647204 - 1716710 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 6p25.3(chr6:647204-1716710)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
    SCV004231427Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Sep 20, 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. 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, SCV004231427.1

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

    Description

    The copy number loss of 6p25.3 involves multiple protein-coding genes, including FOXC1 (OMIM 601090). Haploinsufficiency of FOXC1 is associated with autosomal dominant Axenfeld-Rieger syndrome type 3 (RIEG3; OMIM 602482). Additionally, heterozygous missense and truncating variants of FOXC1 are associated with autosomal dominant anterior segment dysgenesis-3 (ASGD3; OMIM 601631). Larger deletions overlapping the current interval are associated with chromosome 6pter-p24 deletion syndrome (OMIM 612582, Aldinger 2009, Chanda 2008). Additionally, a larger, de novo deletion was identified in an individual with aortic stenosis, global developmental delay and facial dysmorphisms (Ovaert 2017). As there are no similar copy number losses of this region in the general populations of the Database of Genomic Variants, the classification of this copy number variant (CNV) is pathogenic. References: Aldinger et al., Nat Genet. 2009 Sep;41(9):1037-42. PMID: 19668217 Chanda et al., Hum Mol Genet. 2008 Nov 15;17(22):3446-58. PMID: 18694899 Ovaert et al., Am J Med Genet A. 2017 Sep;173(9):2489-2493. PMID: 28657660

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

    Last Updated: Feb 4, 2024