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GRCh37/hg19 3q26.31-29(chr3:174764228-197851986)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 19, 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:
RCV004819300.1

Allele description [Variation Report for GRCh37/hg19 3q26.31-29(chr3:174764228-197851986)x3]

GRCh37/hg19 3q26.31-29(chr3:174764228-197851986)x3

Genes:
  • BDH1:3-hydroxybutyrate dehydrogenase 1 [Gene - OMIM - HGNC]
  • 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]
  • ATP13A3:ATPase 13A3 [Gene - OMIM - HGNC]
  • ATP13A4:ATPase 13A4 [Gene - OMIM - HGNC]
  • ATP13A5:ATPase 13A5 [Gene - OMIM - HGNC]
  • ATP11B:ATPase phospholipid transporting 11B (putative) [Gene - OMIM - HGNC]
  • ACAP2:ArfGAP with coiled-coil, ankyrin repeat and PH domains 2 [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]
  • FBXO45:F-box protein 45 [Gene - OMIM - HGNC]
  • FXR1:FMR1 autosomal homolog 1 [Gene - OMIM - HGNC]
  • GNB4:G protein subunit beta 4 [Gene - OMIM - HGNC]
  • IQCG:IQ motif containing G [Gene - OMIM - HGNC]
  • LPP:LIM domain containing preferred translocation partner in lipoma [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]
  • MB21D2:Mab-21 domain containing 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]
  • OPA1:OPA1 mitochondrial dynamin like GTPase [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]
  • SENP5:SUMO specific peptidase 5 [Gene - OMIM - HGNC]
  • TBCCD1:TBCC domain containing 1 [Gene - OMIM - HGNC]
  • TBL1XR1:TBL1X/Y related 1 [Gene - OMIM - HGNC]
  • TNK2-AS1:TNK2 antisense RNA 1 [Gene - HGNC]
  • UBXN7:UBX domain protein 7 [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]
  • WDR53:WD repeat domain 53 [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]
  • APOD:apolipoprotein D [Gene - OMIM - HGNC]
  • CAMK2N2:calcium/calmodulin dependent protein kinase II inhibitor 2 [Gene - OMIM - HGNC]
  • CPN2:carboxypeptidase N subunit 2 [Gene - OMIM - HGNC]
  • CEP19:centrosomal protein 19 [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]
  • CLDN16:claudin 16 [Gene - OMIM - HGNC]
  • CLDN1:claudin 1 [Gene - OMIM - HGNC]
  • CCDC39:coiled-coil domain 39 molecular ruler complex subunit [Gene - OMIM - HGNC]
  • CCDC50:coiled-coil domain containing 50 [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]
  • DLG1:discs large MAGUK scaffold protein 1 [Gene - OMIM - HGNC]
  • DVL3:dishevelled segment polarity protein 3 [Gene - OMIM - HGNC]
  • DYNLT2B:dynein light chain Tctex-type 2B [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]
  • FAM43A:family with sequence similarity 43 member A [Gene - HGNC]
  • FETUB:fetuin B [Gene - OMIM - HGNC]
  • FGF12:fibroblast growth factor 12 [Gene - OMIM - HGNC]
  • FYTTD1:forty-two-three domain containing 1 [Gene - OMIM - HGNC]
  • GMNC:geminin coiled-coil domain containing [Gene - OMIM - HGNC]
  • GP5:glycoprotein V platelet [Gene - OMIM - HGNC]
  • HES1:hes family bHLH transcription factor 1 [Gene - OMIM - HGNC]
  • HRG:histidine rich glycoprotein [Gene - OMIM - HGNC]
  • IGF2BP2:insulin like growth factor 2 mRNA binding protein 2 [Gene - OMIM - HGNC]
  • IL1RAP:interleukin 1 receptor accessory protein [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]
  • LSG1:large 60S subunit nuclear export GTPase 1 [Gene - OMIM - HGNC]
  • LMLN:leishmanolysin like peptidase [Gene - OMIM - HGNC]
  • LRRC15:leucine rich repeat containing 15 [Gene - OMIM - HGNC]
  • LRCH3:leucine rich repeats and calponin homology domain containing 3 [Gene - HGNC]
  • LIPH:lipase H [Gene - OMIM - HGNC]
  • LAMP3:lysosomal associated membrane protein 3 [Gene - OMIM - HGNC]
  • MELTF:melanotransferrin [Gene - OMIM - HGNC]
  • MCCC1:methylcrotonyl-CoA carboxylase subunit 1 [Gene - OMIM - HGNC]
  • MIR1224:microRNA 1224 [Gene - OMIM - HGNC]
  • MIR28:microRNA 28 [Gene - OMIM - HGNC]
  • MIR570:microRNA 570 [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]
  • MUC20:mucin 20, cell surface associated [Gene - OMIM - HGNC]
  • MUC4:mucin 4, cell surface associated [Gene - OMIM - HGNC]
  • NRROS:negative regulator of reactive oxygen species [Gene - OMIM - HGNC]
  • NCBP2:nuclear cap binding protein subunit 2 [Gene - OMIM - HGNC]
  • OSTN:osteocrin [Gene - OMIM - HGNC]
  • PAK2:p21 (RAC1) activated kinase 2 [Gene - OMIM - HGNC]
  • PEX5L:peroxisomal biogenesis factor 5 like [Gene - OMIM - HGNC]
  • PCYT1A:phosphate cytidylyltransferase 1A, choline [Gene - OMIM - HGNC]
  • PIGX:phosphatidylinositol glycan anchor biosynthesis class X [Gene - OMIM - HGNC]
  • PIGZ:phosphatidylinositol glycan anchor biosynthesis class Z [Gene - OMIM - HGNC]
  • PIK3CA:phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha [Gene - OMIM - HGNC]
  • PLAAT1:phospholipase A and acyltransferase 1 [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]
  • P3H2:prolyl 3-hydroxylase 2 [Gene - OMIM - HGNC]
  • PSMD2:proteasome 26S subunit ubiquitin receptor, non-ATPase 2 [Gene - OMIM - HGNC]
  • PPP1R2:protein phosphatase 1 regulatory inhibitor subunit 2 [Gene - OMIM - HGNC]
  • PYDC2:pyrin domain containing 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]
  • RPL35A:ribosomal protein L35a [Gene - OMIM - HGNC]
  • RPL39L:ribosomal protein L39 like [Gene - OMIM - HGNC]
  • RNF168:ring finger protein 168 [Gene - OMIM - HGNC]
  • RUBCN:rubicon autophagy regulator [Gene - OMIM - HGNC]
  • SMCO1:single-pass membrane protein with coiled-coil domains 1 [Gene - HGNC]
  • SNORA63:small nucleolar RNA, H/ACA box 63 [Gene - OMIM - HGNC]
  • SNORA81:small nucleolar RNA, H/ACA box 81 [Gene - OMIM - HGNC]
  • SLC51A:solute carrier family 51 member A [Gene - OMIM - HGNC]
  • SST:somatostatin [Gene - OMIM - HGNC]
  • TTC14:tetratricopeptide repeat domain 14 [Gene - HGNC]
  • THPO:thrombopoietin [Gene - OMIM - HGNC]
  • TFRC:transferrin receptor [Gene - OMIM - HGNC]
  • TRA2B:transformer 2 beta homolog [Gene - OMIM - HGNC]
  • TM4SF19:transmembrane 4 L six family member 19 [Gene - OMIM - HGNC]
  • TMEM207:transmembrane protein 207 [Gene - OMIM - HGNC]
  • TMEM41A:transmembrane protein 41A [Gene - HGNC]
  • TMEM44:transmembrane protein 44 [Gene - HGNC]
  • TPRG1:tumor protein p63 regulated 1 [Gene - HGNC]
  • TP63:tumor protein p63 [Gene - OMIM - HGNC]
  • TNK2:tyrosine kinase non receptor 2 [Gene - OMIM - HGNC]
  • USP13:ubiquitin specific peptidase 13 [Gene - OMIM - HGNC]
  • UTS2B:urotensin 2B [Gene - OMIM - HGNC]
  • VWA5B2:von Willebrand factor A domain containing 5B2 [Gene - HGNC]
  • XXYLT1:xyloside xylosyltransferase 1 [Gene - OMIM - HGNC]
  • ZDHHC19:zinc finger DHHC-type palmitoyltransferase 19 [Gene - OMIM - 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:
3q26.31-29
Genomic location:
Chr3: 174764228 - 197851986 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 3q26.31-29(chr3:174764228-197851986)x3
HGVS:

    Condition(s)

    Synonyms:
    none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
    Identifiers:
    MedGen: C3661900

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV005439900Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Oct 19, 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. 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, SCV005439900.1

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

    Description

    This duplication involves numerous protein-coding genes and contains the region associated with 3q29 duplication syndrome (OMIM 611936). In addition, duplications of various sizes overlapping the current region have been reported (Dworschak 2017, Pavone 2016, Riehmer 2017, Serra 2023). Thus, based on current medical literature and gene count, this CNV is classified as pathogenic. References: Dworschak et al., Clin Genet. 2017 May;91(5):661-671. PMID: 27549440; Pavone et al., Clin Dysmorphol. 2016 Jul;25(3):121-7. PMID: 26918294; Riehmer et al., Am J Med Genet A. 2017 Aug;173(8):2132-2138. PMID: 28574232; Serra et al., Ital J Pediatr. 2023 Feb 9;49(1):17. PMID: 36759911

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

    Last Updated: Jan 4, 2025