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GRCh37/hg19 9p24.1-22.3(chr9:8595338-15622555)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 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:
RCV003483054.1

Allele description [Variation Report for GRCh37/hg19 9p24.1-22.3(chr9:8595338-15622555)x1]

GRCh37/hg19 9p24.1-22.3(chr9:8595338-15622555)x1

Genes:
  • FREM1:FRAS1 related extracellular matrix 1 [Gene - OMIM - HGNC]
  • PSIP1:PC4 and SRSF1 interacting protein 1 [Gene - OMIM - HGNC]
  • CER1:cerberus 1, DAN family BMP antagonist [Gene - OMIM - HGNC]
  • CCDC171:coiled-coil domain containing 171 [Gene - HGNC]
  • LURAP1L:leucine rich adaptor protein 1 like [Gene - OMIM - HGNC]
  • MPDZ:multiple PDZ domain crumbs cell polarity complex component [Gene - OMIM - HGNC]
  • NFIB:nuclear factor I B [Gene - OMIM - HGNC]
  • PTPRD:protein tyrosine phosphatase receptor type D [Gene - OMIM - HGNC]
  • SNAPC3:small nuclear RNA activating complex polypeptide 3 [Gene - OMIM - HGNC]
  • TTC39B:tetratricopeptide repeat domain 39B [Gene - OMIM - HGNC]
  • TYRP1:tyrosinase related protein 1 [Gene - OMIM - HGNC]
  • ZDHHC21:zinc finger DHHC-type palmitoyltransferase 21 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
9p24.1-22.3
Genomic location:
Chr9: 8595338 - 15622555 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 9p24.1-22.3(chr9:8595338-15622555)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
    SCV004231571Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Aug 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, SCV004231571.1

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

    Description

    The copy number loss of 9p24.1p22.3 involves multiple protein-coding genes, including NFIB (OMIM 600728) and FREM1 (OMIM 608944). Haploinsufficiency of NFIB is associated with autosomal dominant acquired macrocephaly with impaired intellectual development (MACID; OMIM 618286, Barrus 2020, Rao 2020, Schanze 2018, Sajan 2013). Furthermore, the current deletion lies within the larger 9p deletion syndrome interval and falls within proposed critical regions for this syndrome reported in multiple studies (Christ 1999, Hauge 2008, Kawara 2006, Swinkels 2008, OMIM 158170). There are no similar copy number losses of this region in the general populations of the Database of Genomic Variants. Thus, this copy number variant (CNV) is classified as pathogenic. References: Barrus et al., Am J Med Genet A. 2020 Dec;182(12):2959-2963. PMID: 32902921 Christ et al., Am J Hum Genet. 1999 Nov;65(5):1387-95. PMID: 10521304 Hauge et al., Genet Med. 2008 Aug;10(8):599-611. PMID: 18641517 Kawara et al., Am J Med Genet A. 2006 Feb 15;140(4):373-7. PMID: 16419130 Rao et al., Eur J Med Genet. 2020 Dec;63(12):104092. PMID: 33130023 Sajan et al., PLoS Genet. 2013;9(10):e1003823. PMID: 24098143 Schanze et al., Am J Hum Genet. 2018 Nov 1;103(5):752-768. PMID: 30388402 Swinkels et al., Am J Med Genet A. 2008 Jun 1;146A(11):1430-8. PMID: 18452192 Vissers et al., PLoS Genet. 2011 Sep;7(9):e1002278. PMID: 21931569

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

    Last Updated: Feb 4, 2024