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GRCh37/hg19 2q11.1-13(chr2:96353030-114045463)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 31, 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:
RCV000682168.2

Allele description [Variation Report for GRCh37/hg19 2q11.1-13(chr2:96353030-114045463)x3]

GRCh37/hg19 2q11.1-13(chr2:96353030-114045463)x3

Genes:
  • NT5DC4:5'-nucleotidase domain containing 4 [Gene - HGNC]
  • AFF3:ALF transcription elongation factor 3 [Gene - OMIM - HGNC]
  • ARID5A:AT-rich interaction domain 5A [Gene - OMIM - HGNC]
  • BCL2L11:BCL2 like 11 [Gene - OMIM - HGNC]
  • BUB1:BUB1 mitotic checkpoint serine/threonine kinase [Gene - OMIM - HGNC]
  • CNOT11:CCR4-NOT transcription complex subunit 11 [Gene - OMIM - HGNC]
  • CRACDL:CRACD like [Gene - HGNC]
  • ECRG4:ECRG4 augurin precursor [Gene - OMIM - HGNC]
  • GPR45:G protein-coupled receptor 45 [Gene - OMIM - HGNC]
  • GCC2:GRIP and coiled-coil domain containing 2 [Gene - OMIM - HGNC]
  • ITPRIPL1:ITPRIP like 1 [Gene - HGNC]
  • KANSL3:KAT8 regulatory NSL complex subunit 3 [Gene - OMIM - HGNC]
  • LIMS1:LIM zinc finger domain containing 1 [Gene - OMIM - HGNC]
  • LIMS3:LIM zinc finger domain containing 3 [Gene - HGNC]
  • LIMS4:LIM zinc finger domain containing 4 [Gene - HGNC]
  • LONRF2:LON peptidase N-terminal domain and ring finger 2 [Gene - HGNC]
  • MERTK:MER proto-oncogene, tyrosine kinase [Gene - OMIM - HGNC]
  • NCK2:NCK adaptor protein 2 [Gene - OMIM - HGNC]
  • POU3F3:POU class 3 homeobox 3 [Gene - OMIM - HGNC]
  • RANBP2:RAN binding protein 2 [Gene - OMIM - HGNC]
  • RGPD3:RANBP2 like and GRIP domain containing 3 [Gene - OMIM - HGNC]
  • RGPD4:RANBP2 like and GRIP domain containing 4 [Gene - OMIM - HGNC]
  • RGPD5:RANBP2 like and GRIP domain containing 5 [Gene - OMIM - HGNC]
  • RGPD6:RANBP2 like and GRIP domain containing 6 [Gene - OMIM - HGNC]
  • RGPD8:RANBP2 like and GRIP domain containing 8 [Gene - OMIM - HGNC]
  • REV1:REV1 DNA directed polymerase [Gene - OMIM - HGNC]
  • POLR1B:RNA polymerase I subunit B [Gene - OMIM - HGNC]
  • ST6GAL2:ST6 beta-galactoside alpha-2,6-sialyltransferase 2 [Gene - OMIM - HGNC]
  • STARD7:StAR related lipid transfer domain containing 7 [Gene - OMIM - HGNC]
  • TBC1D8:TBC1 domain family member 8 [Gene - HGNC]
  • UXS1:UDP-glucuronate decarboxylase 1 [Gene - OMIM - HGNC]
  • ACTR1B:actin related protein 1B [Gene - OMIM - HGNC]
  • ACOXL:acyl-CoA oxidase like [Gene - HGNC]
  • ADRA2B:adrenoceptor alpha 2B [Gene - OMIM - HGNC]
  • MGAT4A:alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A [Gene - OMIM - HGNC]
  • ANAPC1:anaphase promoting complex subunit 1 [Gene - OMIM - HGNC]
  • ANKRD23:ankyrin repeat domain 23 [Gene - OMIM - HGNC]
  • ANKRD36:ankyrin repeat domain 36 [Gene - OMIM - HGNC]
  • ANKRD36B:ankyrin repeat domain 36B [Gene - HGNC]
  • ANKRD36C:ankyrin repeat domain 36C [Gene - HGNC]
  • ANKRD39:ankyrin repeat domain 39 [Gene - HGNC]
  • ASTL:astacin like metalloendopeptidase [Gene - OMIM - HGNC]
  • CHST10:carbohydrate sulfotransferase 10 [Gene - OMIM - HGNC]
  • CREG2:cellular repressor of E1A stimulated genes 2 [Gene - OMIM - HGNC]
  • C2orf15:chromosome 2 open reading frame 15 [Gene - HGNC]
  • C2orf49:chromosome 2 open reading frame 49 [Gene - HGNC]
  • CCDC138:coiled-coil domain containing 138 [Gene - HGNC]
  • CHCHD5:coiled-coil-helix-coiled-coil-helix domain containing 5 [Gene - OMIM - HGNC]
  • CNGA3:cyclic nucleotide gated channel subunit alpha 3 [Gene - OMIM - HGNC]
  • CNNM3:cyclin and CBS domain divalent metal cation transport mediator 3 [Gene - OMIM - HGNC]
  • CNNM4:cyclin and CBS domain divalent metal cation transport mediator 4 [Gene - OMIM - HGNC]
  • COA5:cytochrome c oxidase assembly factor 5 [Gene - OMIM - HGNC]
  • COX5B:cytochrome c oxidase subunit 5B [Gene - OMIM - HGNC]
  • CKAP2L:cytoskeleton associated protein 2 like [Gene - OMIM - HGNC]
  • CIAO1:cytosolic iron-sulfur assembly component 1 [Gene - OMIM - HGNC]
  • DUSP2:dual specificity phosphatase 2 [Gene - OMIM - HGNC]
  • EDAR:ectodysplasin A receptor [Gene - OMIM - HGNC]
  • EIF5B:eukaryotic translation initiation factor 5B [Gene - OMIM - HGNC]
  • FAM178B:family with sequence similarity 178 member B [Gene - HGNC]
  • FER1L5:fer-1 like family member 5 [Gene - HGNC]
  • FBLN7:fibulin 7 [Gene - OMIM - HGNC]
  • FHL2:four and a half LIM domains 2 [Gene - OMIM - HGNC]
  • FAHD2B:fumarylacetoacetate hydrolase domain containing 2B [Gene - HGNC]
  • GPAT2:glycerol-3-phosphate acyltransferase 2, mitochondrial [Gene - OMIM - HGNC]
  • INPP4A:inositol polyphosphate-4-phosphatase type I A [Gene - OMIM - HGNC]
  • IL1A:interleukin 1 alpha [Gene - OMIM - HGNC]
  • IL1B:interleukin 1 beta [Gene - OMIM - HGNC]
  • IL1F10:interleukin 1 family member 10 [Gene - OMIM - HGNC]
  • IL1RN:interleukin 1 receptor antagonist [Gene - OMIM - HGNC]
  • IL1RL1:interleukin 1 receptor like 1 [Gene - OMIM - HGNC]
  • IL1RL2:interleukin 1 receptor like 2 [Gene - OMIM - HGNC]
  • IL1R1:interleukin 1 receptor type 1 [Gene - OMIM - HGNC]
  • IL1R2:interleukin 1 receptor type 2 [Gene - OMIM - HGNC]
  • IL18R1:interleukin 18 receptor 1 [Gene - OMIM - HGNC]
  • IL18RAP:interleukin 18 receptor accessory protein [Gene - OMIM - HGNC]
  • IL36A:interleukin 36 alpha [Gene - OMIM - HGNC]
  • IL36B:interleukin 36 beta [Gene - OMIM - HGNC]
  • IL36G:interleukin 36 gamma [Gene - OMIM - HGNC]
  • IL36RN:interleukin 36 receptor antagonist [Gene - OMIM - HGNC]
  • IL37:interleukin 37 [Gene - OMIM - HGNC]
  • LMAN2L:lectin, mannose binding 2 like [Gene - OMIM - HGNC]
  • LIPT1:lipoyltransferase 1 [Gene - OMIM - HGNC]
  • LYG1:lysozyme g1 [Gene - HGNC]
  • LYG2:lysozyme g2 [Gene - OMIM - HGNC]
  • MFSD9:major facilitator superfamily domain containing 9 [Gene - OMIM - HGNC]
  • MALL:mal, T cell differentiation protein like [Gene - OMIM - HGNC]
  • MITD1:microtubule interacting and trafficking domain containing 1 [Gene - HGNC]
  • MRPL30:mitochondrial ribosomal protein L30 [Gene - OMIM - HGNC]
  • MRPS9:mitochondrial ribosomal protein S9 [Gene - OMIM - HGNC]
  • MAP4K4:mitogen-activated protein kinase kinase kinase kinase 4 [Gene - OMIM - HGNC]
  • NPHP1:nephrocystin 1 [Gene - OMIM - HGNC]
  • NMS:neuromedin S [Gene - OMIM - HGNC]
  • NPAS2:neuronal PAS domain protein 2 [Gene - OMIM - HGNC]
  • NCAPH:non-SMC condensin I complex subunit H [Gene - OMIM - HGNC]
  • PAX8:paired box 8 [Gene - OMIM - HGNC]
  • PDCL3:phosducin like 3 [Gene - OMIM - HGNC]
  • PSD4:pleckstrin and Sec7 domain containing 4 [Gene - OMIM - HGNC]
  • RFX8:regulatory factor X8 [Gene - HGNC]
  • RPL31:ribosomal protein L31 [Gene - OMIM - HGNC]
  • RNF149:ring finger protein 149 [Gene - HGNC]
  • SEMA4C:semaphorin 4C [Gene - OMIM - HGNC]
  • SEPTIN10:septin 10 [Gene - OMIM - HGNC]
  • SNRNP200:small nuclear ribonucleoprotein U5 subunit 200 [Gene - OMIM - HGNC]
  • SLC20A1:solute carrier family 20 member 1 [Gene - OMIM - HGNC]
  • SLC5A7:solute carrier family 5 member 7 [Gene - OMIM - HGNC]
  • SLC9A2:solute carrier family 9 member A2 [Gene - OMIM - HGNC]
  • SLC9A4:solute carrier family 9 member A4 [Gene - OMIM - HGNC]
  • SOWAHC:sosondowah ankyrin repeat domain family member C [Gene - HGNC]
  • SULT1C2:sulfotransferase family 1C member 2 [Gene - OMIM - HGNC]
  • SULT1C3:sulfotransferase family 1C member 3 [Gene - OMIM - HGNC]
  • SULT1C4:sulfotransferase family 1C member 4 [Gene - OMIM - HGNC]
  • TSGA10:testis specific 10 [Gene - OMIM - HGNC]
  • TXNDC9:thioredoxin domain containing 9 [Gene - OMIM - HGNC]
  • TGFBRAP1:transforming growth factor beta receptor associated protein 1 [Gene - OMIM - HGNC]
  • TMEM127:transmembrane protein 127 [Gene - OMIM - HGNC]
  • TMEM131:transmembrane protein 131 [Gene - OMIM - HGNC]
  • TMEM182:transmembrane protein 182 [Gene - HGNC]
  • TMEM87B:transmembrane protein 87B [Gene - OMIM - HGNC]
  • TTL:tubulin tyrosine ligase [Gene - OMIM - HGNC]
  • UNC50:unc-50 inner nuclear membrane RNA binding protein [Gene - OMIM - HGNC]
  • VWA3B:von Willebrand factor A domain containing 3B [Gene - OMIM - HGNC]
  • ZAP70:zeta chain of T cell receptor associated protein kinase 70 [Gene - OMIM - HGNC]
  • ZC3H6:zinc finger CCCH-type containing 6 [Gene - HGNC]
  • ZC3H8:zinc finger CCCH-type containing 8 [Gene - HGNC]
Variant type:
copy number gain
Cytogenetic location:
2q11.1-13
Genomic location:
Chr2: 96353030 - 114045463 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 2q11.1-13(chr2:96353030-114045463)x3
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
    SCV000809675Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Aug 31, 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, SCV000809675.2

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

    Description

    The copy number gain of 2q11.1q13 involves 129 protein-coding genes. Duplications of single or multiple cytobands from 2q11.1 to 2q13 have been reported in numerous cases of patients with neurological, gastrointestinal, and congenital anomalies (Aarabi 2022, Riley 2015, Rudd 2009, Chen 2020). Rudd et al. (2009), however, did suggest that duplications of 2q13 may demonstrate reduced penetrance based on observations in phenotypically normal individuals. There are no similar copy number gains of this region in the general populations of the Database of Genomic Variants. Thus, based on current medical literature and gene content, this copy number variant (CNV) is classified as pathogenic. References: Aarabi et al., Psychiatr Genet. 2022 Jul 15. PMID: 35837682 Chen et al., Taiwan J Obstet Gynecol. 2020 Nov;59(6):941-944. PMID: 33218417 Riley et al., Am J Med Genet A. 2015 Nov;167A(11):2664-73. PMID: 26227573 Rudd et al., Hum Mol Genet. 2009 Aug 15;18(16):2957-62. PMID: 19443486

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

    Last Updated: Feb 4, 2024