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GRCh37/hg19 13q32.3-34(chr13:99421603-115107733)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 6, 2021
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:
RCV002475671.1

Allele description [Variation Report for GRCh37/hg19 13q32.3-34(chr13:99421603-115107733)x3]

GRCh37/hg19 13q32.3-34(chr13:99421603-115107733)x3

Genes:
  • ADPRHL1:ADP-ribosylhydrolase like 1 [Gene - OMIM - HGNC]
  • ANKRD10-IT1:ANKRD10 intronic transcript 1 [Gene - HGNC]
  • ATP11AUN:ATP11A upstream neighbor lncRNA [Gene - HGNC]
  • ATP4B:ATPase H+/K+ transporting subunit beta [Gene - OMIM - HGNC]
  • ATP11A:ATPase phospholipid transporting 11A [Gene - OMIM - HGNC]
  • BIVM-ERCC5:BIVM-ERCC5 readthrough [Gene - HGNC]
  • DAOA:D-amino acid oxidase activator [Gene - OMIM - HGNC]
  • DAOA-AS1:DAOA antisense RNA 1 [Gene - OMIM - HGNC]
  • LIG4:DNA ligase 4 [Gene - OMIM - HGNC]
  • ERCC5:ERCC excision repair 5, endonuclease [Gene - OMIM - HGNC]
  • GPR183:G protein-coupled receptor 183 [Gene - OMIM - HGNC]
  • GPR18:G protein-coupled receptor 18 [Gene - OMIM - HGNC]
  • MCF2L:MCF.2 cell line derived transforming sequence like [Gene - OMIM - HGNC]
  • NAXD:NAD(P)HX dehydratase [Gene - OMIM - HGNC]
  • NALF1:NALCN channel auxiliary factor 1 [Gene - OMIM - HGNC]
  • PCID2:PCI domain containing 2 [Gene - OMIM - HGNC]
  • RAB20:RAB20, member RAS oncogene family [Gene - HGNC]
  • RASA3:RAS p21 protein activator 3 [Gene - OMIM - HGNC]
  • ARHGEF7:Rho guanine nucleotide exchange factor 7 [Gene - OMIM - HGNC]
  • SOX1:SRY-box transcription factor 1 [Gene - OMIM - HGNC]
  • SWINGN:SWI/SNF complex interacting GAS6 enhancer non-coding RNA [Gene - HGNC]
  • TNFSF13B:TNF superfamily member 13b [Gene - OMIM - HGNC]
  • UBAC2:UBA domain containing 2 [Gene - HGNC]
  • UPF3A:UPF3A regulator of nonsense mediated mRNA decay [Gene - OMIM - HGNC]
  • ZIC2:Zic family member 2 [Gene - OMIM - HGNC]
  • ZIC5:Zic family member 5 [Gene - OMIM - HGNC]
  • ABHD13:abhydrolase domain containing 13 [Gene - HGNC]
  • ANKRD10:ankyrin repeat domain 10 [Gene - HGNC]
  • ARGLU1:arginine and glutamate rich 1 [Gene - OMIM - HGNC]
  • BIVM:basic, immunoglobulin-like variable motif containing [Gene - OMIM - HGNC]
  • CDC16:cell division cycle 16 [Gene - OMIM - HGNC]
  • CHAMP1:chromosome alignment maintaining phosphoprotein 1 [Gene - OMIM - HGNC]
  • CLYBL:citramalyl-CoA lyase [Gene - OMIM - HGNC]
  • F7:coagulation factor VII [Gene - OMIM - HGNC]
  • F10:coagulation factor X [Gene - OMIM - HGNC]
  • CCDC168:coiled-coil domain containing 168 [Gene - HGNC]
  • COL4A1:collagen type IV alpha 1 chain [Gene - OMIM - HGNC]
  • COL4A2:collagen type IV alpha 2 chain [Gene - OMIM - HGNC]
  • CUL4A:cullin 4A [Gene - OMIM - HGNC]
  • CARS2:cysteinyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
  • DOCK9:dedicator of cytokinesis 9 [Gene - OMIM - HGNC]
  • DCUN1D2:defective in cullin neddylation 1 domain containing 2 [Gene - HGNC]
  • EFNB2:ephrin B2 [Gene - OMIM - HGNC]
  • FGF14:fibroblast growth factor 14 [Gene - OMIM - HGNC]
  • GGACT:gamma-glutamylamine cyclotransferase [Gene - OMIM - HGNC]
  • GAS6:growth arrest specific 6 [Gene - OMIM - HGNC]
  • GRTP1:growth hormone regulated TBC protein 1 [Gene - HGNC]
  • ING1:inhibitor of growth family member 1 [Gene - OMIM - HGNC]
  • IRS2:insulin receptor substrate 2 [Gene - OMIM - HGNC]
  • ITGBL1:integrin subunit beta like 1 [Gene - OMIM - HGNC]
  • LINC00567:long intergenic non-protein coding RNA 567 [Gene - HGNC]
  • LAMP1:lysosomal associated membrane protein 1 [Gene - OMIM - HGNC]
  • METTL21C:methyltransferase 21C, AARS1 lysine [Gene - OMIM - HGNC]
  • MYO16:myosin XVI [Gene - OMIM - HGNC]
  • PCCA:propionyl-CoA carboxylase subunit alpha [Gene - OMIM - HGNC]
  • POGLUT2:protein O-glucosyltransferase 2 [Gene - OMIM - HGNC]
  • PROZ:protein Z, vitamin K dependent plasma glycoprotein [Gene - OMIM - HGNC]
  • NALCN:sodium leak channel, non-selective [Gene - OMIM - HGNC]
  • SLC10A2:solute carrier family 10 member 2 [Gene - OMIM - HGNC]
  • SPACA7:sperm acrosome associated 7 [Gene - HGNC]
  • TEX29:testis expressed 29 [Gene - HGNC]
  • TEX30:testis expressed 30 [Gene - HGNC]
  • TFDP1:transcription factor Dp-1 [Gene - OMIM - HGNC]
  • TM9SF2:transmembrane 9 superfamily member 2 [Gene - OMIM - HGNC]
  • TMTC4:transmembrane O-mannosyltransferase targeting cadherins 4 [Gene - OMIM - HGNC]
  • TMCO3:transmembrane and coiled-coil domains 3 [Gene - OMIM - HGNC]
  • TMEM255B:transmembrane protein 255B [Gene - HGNC]
  • TPP2:tripeptidyl peptidase 2 [Gene - OMIM - HGNC]
  • TUBGCP3:tubulin gamma complex associated protein 3 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
13q32.3-34
Genomic location:
Chr13: 99421603 - 115107733 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 13q32.3-34(chr13:99421603-115107733)x3
HGVS:

    Condition(s)

    Synonyms:
    none provided
    Identifiers:
    MedGen: CN517202

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV002772899Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Oct 6, 2021)     		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, SCV002772899.1

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

    Description

    The copy number gain of 13q32.3qter involves numerous protein coding genes including COL4A1 (OMIM 120130), COL4A2 (OMIM 120090) and is expected to cause phenotypic and/or developmental abnormalities. A de novo heterozygous duplication of 13q32q34 was reported in a patient with developmental delay, seizures, mild dysmorphism, and hypotonia (Milani 2006). The authors reported absence of the cardinal features of trisomy 13, such as brain malformation, polydactyly, hernias, urogenital abnormalities, and hemangiomas, in their patient. Moreover, a smaller 8.1 Mb duplication at 13q33.2q34 including COL4A1 and COL4A2 was reported in an adult patient with periventricular leukoencephalopathy and cerebral small vessel disease (Renard 2014). Further, de novo supernumerary marker chromosomes (sSMCs), leading to gains of 13q32qter locus, are reported in patients with common manifestations including hemangioma, low set or abnormal ears, dysmorphic eyes and ophthalmologic diseases, developmental delay, intellectual disability, and facial dysmorphism (Liu 2013; Barwell 2004; Warburton 2000). This large duplication also includes multiple genes that are associated with autosomal dominant OMIM phenotype: ZIC2 (OMIM 609637), NALCN (OMIM 616266), FGF14 (OMIM 609307), IRS2 (OMIM 125853), COL4A1 (OMIMs 180000, 614519, 611773, 175780, and 618564), COL4A2(OMIMs 614519 and 614483), and CHAMP1 (OMIM 616579)._x000D__x000D_ Reference_x000D__x000D_ Barwell et al., Am J Med Genet A. 2004 Oct 15;130A(3):295-8. PMID: 15378552._x000D__x000D_ Liu et al., Birth Defects Res A Clin Mol Teratol. 2013 Dec;97(12):812-5. PMID: 24222317._x000D__x000D_ Milani et al., J Child Neurol. 2006 Dec;21(12):1084-5. PMID: 17156706. _x000D__x000D_ Renard et al., Neurology. 2014 Sep 9;83(11):1029-31. PMID: 25098541._x000D__x000D_ Warburton et al., Am J Hum Genet. 2000 Jun;66(6):1794-806. PMID: 10777715._x000D__x000D_

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

    Last Updated: Mar 26, 2023