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GRCh37/hg19 4q12-13.3(chr4:57584845-72430996)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 1, 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:
RCV003485417.1

Allele description [Variation Report for GRCh37/hg19 4q12-13.3(chr4:57584845-72430996)x1]

GRCh37/hg19 4q12-13.3(chr4:57584845-72430996)x1

Genes:
  • EPHA5:EPH receptor A5 [Gene - OMIM - HGNC]
  • GRSF1:G-rich RNA sequence binding factor 1 [Gene - OMIM - HGNC]
  • MOB1B:MOB kinase activator 1B [Gene - OMIM - HGNC]
  • REST:RE1 silencing transcription factor [Gene - OMIM - HGNC]
  • POLR2B:RNA polymerase II subunit B [Gene - OMIM - HGNC]
  • RUFY3:RUN and FYVE domain containing 3 [Gene - OMIM - HGNC]
  • UGT2A1:UDP glucuronosyltransferase family 2 member A1 complex locus [Gene - OMIM - HGNC]
  • UGT2A2:UDP glucuronosyltransferase family 2 member A2 [Gene - OMIM - HGNC]
  • UGT2A3:UDP glucuronosyltransferase family 2 member A3 [Gene - OMIM - HGNC]
  • UGT2B10:UDP glucuronosyltransferase family 2 member B10 [Gene - OMIM - HGNC]
  • UGT2B11:UDP glucuronosyltransferase family 2 member B11 [Gene - OMIM - HGNC]
  • UGT2B15:UDP glucuronosyltransferase family 2 member B15 [Gene - OMIM - HGNC]
  • UGT2B17:UDP glucuronosyltransferase family 2 member B17 [Gene - OMIM - HGNC]
  • UGT2B28:UDP glucuronosyltransferase family 2 member B28 [Gene - OMIM - HGNC]
  • UGT2B4:UDP glucuronosyltransferase family 2 member B4 [Gene - OMIM - HGNC]
  • UGT2B7:UDP glucuronosyltransferase family 2 member B7 [Gene - OMIM - HGNC]
  • UTP3:UTP3 small subunit processome component [Gene - OMIM - HGNC]
  • YTHDC1:YTH N6-methyladenosine RNA binding protein C1 [Gene - OMIM - HGNC]
  • ADGRL3:adhesion G protein-coupled receptor L3 [Gene - OMIM - HGNC]
  • AMBN:ameloblastin [Gene - OMIM - HGNC]
  • AMTN:amelotin [Gene - OMIM - HGNC]
  • CABS1:calcium binding protein, spermatid associated 1 [Gene - OMIM - HGNC]
  • CSN1S1:casein alpha s1 [Gene - OMIM - HGNC]
  • CSN2:casein beta [Gene - OMIM - HGNC]
  • CSN3:casein kappa [Gene - OMIM - HGNC]
  • CENPC:centromere protein C [Gene - OMIM - HGNC]
  • DCK:deoxycytidine kinase [Gene - OMIM - HGNC]
  • ENAM:enamelin [Gene - OMIM - HGNC]
  • FDCSP:follicular dendritic cell secreted protein [Gene - OMIM - HGNC]
  • GNRHR:gonadotropin releasing hormone receptor [Gene - OMIM - HGNC]
  • HTN1:histatin 1 [Gene - OMIM - HGNC]
  • HTN3:histatin 3 [Gene - OMIM - HGNC]
  • IGFBP7:insulin like growth factor binding protein 7 [Gene - OMIM - HGNC]
  • JCHAIN:joining chain of multimeric IgA and IgM [Gene - OMIM - HGNC]
  • MUC7:mucin 7, secreted [Gene - OMIM - HGNC]
  • NOA1:nitric oxide associated 1 [Gene - OMIM - HGNC]
  • ODAM:odontogenic, ameloblast associated [Gene - OMIM - HGNC]
  • OPRPN:opiorphin prepropeptide [Gene - OMIM - HGNC]
  • PRR27:proline rich 27 [Gene - HGNC]
  • SPINK2:serine peptidase inhibitor Kazal type 2 [Gene - OMIM - HGNC]
  • STAP1:signal transducing adaptor family member 1 [Gene - OMIM - HGNC]
  • SLC4A4:solute carrier family 4 member 4 [Gene - OMIM - HGNC]
  • STATH:statherin [Gene - OMIM - HGNC]
  • SMR3A:submaxillary gland androgen regulated protein 3A [Gene - OMIM - HGNC]
  • SMR3B:submaxillary gland androgen regulated protein 3B [Gene - OMIM - HGNC]
  • SULT1B1:sulfotransferase family 1B member 1 [Gene - OMIM - HGNC]
  • SULT1E1:sulfotransferase family 1E member 1 [Gene - OMIM - HGNC]
  • TECRL:trans-2,3-enoyl-CoA reductase like [Gene - OMIM - HGNC]
  • TMPRSS11A:transmembrane serine protease 11A [Gene - OMIM - HGNC]
  • TMPRSS11B:transmembrane serine protease 11B [Gene - HGNC]
  • TMPRSS11D:transmembrane serine protease 11D [Gene - OMIM - HGNC]
  • TMPRSS11E:transmembrane serine protease 11E [Gene - OMIM - HGNC]
  • TMPRSS11F:transmembrane serine protease 11F [Gene - HGNC]
  • UBA6:ubiquitin like modifier activating enzyme 6 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
4q12-13.3
Genomic location:
Chr4: 57584845 - 72430996 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 4q12-13.3(chr4:57584845-72430996)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
    SCV004231343Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Jun 1, 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.

    PubMed [citation]
    PMID:
    31690835
    PMCID:
    PMC7313390

    Details of each submission

    From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004231343.1

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

    Description

    The 4q12q13.3 deletion involves more than 50 protein-coding genes. Deletions overlapping the current interval have been reported in individuals with variable phenotypes (Carter 2017, Chen 2011, Hemati 2014, Hyder 2021, Quintela 2015). In addition, heterozygous variants of REST have been associated with autosomal dominant gingival fibromatosis 5 (GINGF5; OMIM 617626), autosomal dominant deafness 27 (DFNA27; OMIM 612431), and increased susceptibility to Wilms tumor (OMIM 616806). A smaller deletion was identified in an infant (Hyder 2021). There are no similar copy number losses of 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: _x000D__x000D_ Carter et al., Case Rep Genet. 2017;2017:4894515. PMID: 28819573_x000D__x000D_ Chen et al., Genet Couns. 2011;22(3):255-61. PMID: 22029166_x000D__x000D_ Hemati et al., Am J Med Genet A. 2015 Jan;167A(1):231-7. doi: 10.1002/ajmg.a.36821. Epub 2014 Oct 29. PMID: 25355368_x000D__x000D_ Hyder et al., J Med Genet. 2021 Sep;58(9):581-585. PMID: 32917767_x000D__x000D_ Quintela et al., Am J Med Genet A. 2015 Dec;167A(12):3113-20. PMID: 26284580

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

    Last Updated: Feb 4, 2024