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GRCh37/hg19 3q26.31-27.3(chr3:175119199-187592480)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 18, 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:
RCV001795540.4

Allele description [Variation Report for GRCh37/hg19 3q26.31-27.3(chr3:175119199-187592480)x3]

GRCh37/hg19 3q26.31-27.3(chr3:175119199-187592480)x3

Genes:
  • HTR3C:5-hydroxytryptamine receptor 3C [Gene - OMIM - HGNC]
  • HTR3D:5-hydroxytryptamine receptor 3D [Gene - OMIM - HGNC]
  • HTR3E:5-hydroxytryptamine receptor 3E [Gene - OMIM - HGNC]
  • ALG3:ALG3 alpha-1,3- mannosyltransferase [Gene - OMIM - HGNC]
  • ABCC5:ATP binding cassette subfamily C member 5 [Gene - OMIM - HGNC]
  • ABCF3:ATP binding cassette subfamily F member 3 [Gene - OMIM - HGNC]
  • ATP11B:ATPase phospholipid transporting 11B (putative) [Gene - OMIM - HGNC]
  • BCL6:BCL6 transcription repressor [Gene - OMIM - HGNC]
  • DNAJB11:DnaJ heat shock protein family (Hsp40) member B11 [Gene - OMIM - HGNC]
  • DNAJC19:DnaJ heat shock protein family (Hsp40) member C19 [Gene - OMIM - HGNC]
  • EPHB3:EPH receptor B3 [Gene - OMIM - HGNC]
  • ETV5:ETS variant transcription factor 5 [Gene - OMIM - HGNC]
  • FXR1:FMR1 autosomal homolog 1 [Gene - OMIM - HGNC]
  • GNB4:G protein subunit beta 4 [Gene - OMIM - HGNC]
  • MAGEF1:MAGE family member F1 [Gene - OMIM - HGNC]
  • MAP6D1:MAP6 domain containing 1 [Gene - OMIM - HGNC]
  • MASP1:MBL associated serine protease 1 [Gene - OMIM - HGNC]
  • MCF2L2:MCF.2 cell line derived transforming sequence-like 2 [Gene - OMIM - HGNC]
  • NAALADL2:N-acetylated alpha-linked acidic dipeptidase like 2 [Gene - OMIM - HGNC]
  • NDUFB5:NADH:ubiquinone oxidoreductase subunit B5 [Gene - OMIM - HGNC]
  • POLR2H:RNA polymerase II, I and III subunit H [Gene - OMIM - HGNC]
  • SOX2-OT:SOX2 overlapping transcript [Gene - OMIM - HGNC]
  • SOX2:SRY-box transcription factor 2 [Gene - OMIM - HGNC]
  • ST6GAL1:ST6 beta-galactoside alpha-2,6-sialyltransferase 1 [Gene - OMIM - HGNC]
  • SENP2:SUMO specific peptidase 2 [Gene - OMIM - HGNC]
  • TBCCD1:TBCC domain containing 1 [Gene - OMIM - HGNC]
  • TBL1XR1:TBL1X/Y related 1 [Gene - OMIM - HGNC]
  • B3GNT5:UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5 [Gene - OMIM - HGNC]
  • VPS8:VPS8 subunit of CORVET complex [Gene - OMIM - HGNC]
  • YEATS2:YEATS domain containing 2 [Gene - OMIM - HGNC]
  • ACTL6A:actin like 6A [Gene - OMIM - HGNC]
  • AP2M1:adaptor related protein complex 2 subunit mu 1 [Gene - OMIM - HGNC]
  • ADIPOQ:adiponectin, C1Q and collagen domain containing [Gene - OMIM - HGNC]
  • AHSG:alpha 2-HS glycoprotein [Gene - OMIM - HGNC]
  • CAMK2N2:calcium/calmodulin dependent protein kinase II inhibitor 2 [Gene - OMIM - HGNC]
  • CLCN2:chloride voltage-gated channel 2 [Gene - OMIM - HGNC]
  • CHRD:chordin [Gene - OMIM - HGNC]
  • C3orf70:chromosome 3 open reading frame 70 [Gene - HGNC]
  • CCDC39:coiled-coil domain containing 39 [Gene - OMIM - HGNC]
  • CRYGS:crystallin gamma S [Gene - OMIM - HGNC]
  • DCUN1D1:defective in cullin neddylation 1 domain containing 1 [Gene - OMIM - HGNC]
  • DGKG:diacylglycerol kinase gamma [Gene - OMIM - HGNC]
  • DVL3:dishevelled segment polarity protein 3 [Gene - OMIM - HGNC]
  • ECE2:endothelin converting enzyme 2 [Gene - OMIM - HGNC]
  • EHHADH:enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase [Gene - OMIM - HGNC]
  • EIF2B5:eukaryotic translation initiation factor 2B subunit epsilon [Gene - OMIM - HGNC]
  • EIF4G1:eukaryotic translation initiation factor 4 gamma 1 [Gene - OMIM - HGNC]
  • EIF4A2:eukaryotic translation initiation factor 4A2 [Gene - OMIM - HGNC]
  • FAM131A:family with sequence similarity 131 member A [Gene - HGNC]
  • FETUB:fetuin B [Gene - OMIM - HGNC]
  • HRG:histidine rich glycoprotein [Gene - OMIM - HGNC]
  • IGF2BP2:insulin like growth factor 2 mRNA binding protein 2 [Gene - OMIM - HGNC]
  • KLHL24:kelch like family member 24 [Gene - OMIM - HGNC]
  • KLHL6:kelch like family member 6 [Gene - OMIM - HGNC]
  • KNG1:kininogen 1 [Gene - OMIM - HGNC]
  • LIPH:lipase H [Gene - OMIM - HGNC]
  • LAMP3:lysosomal associated membrane protein 3 [Gene - OMIM - HGNC]
  • MCCC1:methylcrotonyl-CoA carboxylase subunit 1 [Gene - OMIM - HGNC]
  • MIR1224:microRNA 1224 [Gene - OMIM - HGNC]
  • MRPL47:mitochondrial ribosomal protein L47 [Gene - OMIM - HGNC]
  • MFN1:mitofusin 1 [Gene - OMIM - HGNC]
  • MAP3K13:mitogen-activated protein kinase kinase kinase 13 [Gene - OMIM - HGNC]
  • PEX5L:peroxisomal biogenesis factor 5 like [Gene - OMIM - HGNC]
  • PIK3CA:phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha [Gene - OMIM - HGNC]
  • KCNMB2:potassium calcium-activated channel subfamily M regulatory beta subunit 2 [Gene - OMIM - HGNC]
  • KCNMB3:potassium calcium-activated channel subfamily M regulatory beta subunit 3 [Gene - OMIM - HGNC]
  • PARL:presenilin associated rhomboid like [Gene - OMIM - HGNC]
  • PSMD2:proteasome 26S subunit ubiquitin receptor, non-ATPase 2 [Gene - OMIM - HGNC]
  • RTP1:receptor transporter protein 1 [Gene - OMIM - HGNC]
  • RTP2:receptor transporter protein 2 [Gene - OMIM - HGNC]
  • RTP4:receptor transporter protein 4 [Gene - OMIM - HGNC]
  • RFC4:replication factor C subunit 4 [Gene - OMIM - HGNC]
  • RPL39L:ribosomal protein L39 like [Gene - OMIM - HGNC]
  • SNORA63:small nucleolar RNA, H/ACA box 63 [Gene - OMIM - HGNC]
  • SNORA81:small nucleolar RNA, H/ACA box 81 [Gene - OMIM - HGNC]
  • SST:somatostatin [Gene - OMIM - HGNC]
  • TTC14:tetratricopeptide repeat domain 14 [Gene - HGNC]
  • THPO:thrombopoietin [Gene - OMIM - HGNC]
  • TRA2B:transformer 2 beta homolog [Gene - OMIM - HGNC]
  • TMEM41A:transmembrane protein 41A [Gene - HGNC]
  • USP13:ubiquitin specific peptidase 13 [Gene - OMIM - HGNC]
  • VWA5B2:von Willebrand factor A domain containing 5B2 [Gene - HGNC]
  • ZMAT3:zinc finger matrin-type 3 [Gene - OMIM - HGNC]
  • ZNF639:zinc finger protein 639 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
3q26.31-27.3
Genomic location:
Chr3: 175119199 - 187592480 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 3q26.31-27.3(chr3:175119199-187592480)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
    SCV002034743Illumina Laboratory Services, Illumina
    criteria provided, single submitter

    (ICSL CNVClassificationCriteria Aug2020)    		Pathogenic
    (Oct 18, 2021)     		unknownclinical testing

    PubMed (2)
    [See all records that cite these PMIDs]

    Citation Link

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

    Citations

    PubMed

    DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.

    Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP.

    Am J Hum Genet. 2009 Apr;84(4):524-33. doi: 10.1016/j.ajhg.2009.03.010. Epub 2009 Apr 2.

    PubMed [citation]
    PMID:
    19344873
    PMCID:
    PMC2667985

    Comprehensive review of the duplication 3q syndrome and report of a patient with Currarino syndrome and de novo duplication 3q26.32-q27.2.

    Dworschak GC, Crétolle C, Hilger A, Engels H, Korsch E, Reutter H, Ludwig M.

    Clin Genet. 2017 May;91(5):661-671. doi: 10.1111/cge.12848. Epub 2016 Oct 10. Review.

    PubMed [citation]
    PMID:
    27549440

    Details of each submission

    From Illumina Laboratory Services, Illumina, SCV002034743.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedclinical testing PubMed (2)

    Description

    This CNV is a 12.4 Mb duplication of 3q26.31-q27.3 on chromosome 3, (seq[GRCh37]dup(3)(q26.31q27.3); chr3:g.175119199_187592480dup), that was identified in a de novo state. This CNV constitutes a gain encompassing 81 protein-coding genes. At least one individual with a similar de novo gain presenting with dysmorphic features and musculoskeletal system abnormalities has been reported in the DECIPHER database (Firth et al. 2009). Dwarschak et al. (2017) present a review of individuals reported in the literature with partial duplications of 3q. The sizes of CNVs varies among reported individuals as well as the clinical presentation. Common recurrent features include microcephaly, intellectual disability, growth retardation, hypotonia, genitourinary anomalies, abnormalities of the hands and feet, renal anomalies, congenital heart defects, and variable facial dysmorphism. Brain anomalies and seizures were also reported. Based on the available evidence, this CNV is classified as pathogenic.

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

    Last Updated: Apr 9, 2023