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GRCh37/hg19 2q36.2-37.3(chr2:225995545-237594511)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 20, 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:
RCV003484091.1

Allele description [Variation Report for GRCh37/hg19 2q36.2-37.3(chr2:225995545-237594511)x3]

GRCh37/hg19 2q36.2-37.3(chr2:225995545-237594511)x3

Genes:
  • HTR2B:5-hydroxytryptamine receptor 2B [Gene - OMIM - HGNC]
  • ARL4C:ADP ribosylation factor like GTPase 4C [Gene - OMIM - HGNC]
  • AGFG1:ArfGAP with FG repeats 1 [Gene - OMIM - HGNC]
  • AGAP1:ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 [Gene - OMIM - HGNC]
  • CCL20:C-C motif chemokine ligand 20 [Gene - OMIM - HGNC]
  • COPS7B:COP9 signalosome subunit 7B [Gene - OMIM - HGNC]
  • DIS3L2:DIS3 like 3'-5' exoribonuclease 2 [Gene - OMIM - HGNC]
  • DNAJB3:DnaJ heat shock protein family (Hsp40) member B3 [Gene - HGNC]
  • EFHD1:EF-hand domain family member D1 [Gene - OMIM - HGNC]
  • FBXO36:F-box protein 36 [Gene - OMIM - HGNC]
  • GPR55:G protein-coupled receptor 55 [Gene - OMIM - HGNC]
  • GIGYF2:GRB10 interacting GYF protein 2 [Gene - OMIM - HGNC]
  • HJURP:Holliday junction recognition protein [Gene - OMIM - HGNC]
  • IQCA1:IQ motif containing with AAA domain 1 [Gene - HGNC]
  • SAG:S-antigen visual arrestin [Gene - OMIM - HGNC]
  • SH3BP4:SH3 domain binding protein 4 [Gene - OMIM - HGNC]
  • SP100:SP100 nuclear antigen [Gene - OMIM - HGNC]
  • SP110:SP110 nuclear body protein [Gene - OMIM - HGNC]
  • SP140L:SP140 nuclear body protein like [Gene - OMIM - HGNC]
  • SP140:SP140 nuclear body protein [Gene - OMIM - HGNC]
  • SPHKAP:SPHK1 interactor, AKAP domain containing [Gene - OMIM - HGNC]
  • UGT1A10:UDP glucuronosyltransferase family 1 member A10 [Gene - OMIM - HGNC]
  • UGT1A1:UDP glucuronosyltransferase family 1 member A1 [Gene - OMIM - HGNC]
  • UGT1A3:UDP glucuronosyltransferase family 1 member A3 [Gene - OMIM - HGNC]
  • UGT1A4:UDP glucuronosyltransferase family 1 member A4 [Gene - OMIM - HGNC]
  • UGT1A5:UDP glucuronosyltransferase family 1 member A5 [Gene - OMIM - HGNC]
  • UGT1A6:UDP glucuronosyltransferase family 1 member A6 [Gene - OMIM - HGNC]
  • UGT1A7:UDP glucuronosyltransferase family 1 member A7 [Gene - OMIM - HGNC]
  • UGT1A8:UDP glucuronosyltransferase family 1 member A8 [Gene - OMIM - HGNC]
  • UGT1A9:UDP glucuronosyltransferase family 1 member A9 [Gene - OMIM - HGNC]
  • B3GNT7:UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7 [Gene - OMIM - HGNC]
  • ALPG:alkaline phosphatase, germ cell [Gene - OMIM - HGNC]
  • ALPI:alkaline phosphatase, intestinal [Gene - OMIM - HGNC]
  • ALPP:alkaline phosphatase, placental [Gene - OMIM - HGNC]
  • ASB18:ankyrin repeat and SOCS box containing 18 [Gene - HGNC]
  • ARMC9:armadillo repeat containing 9 [Gene - OMIM - HGNC]
  • ACKR3:atypical chemokine receptor 3 [Gene - OMIM - HGNC]
  • ATG16L1:autophagy related 16 like 1 [Gene - OMIM - HGNC]
  • CAB39:calcium binding protein 39 [Gene - OMIM - HGNC]
  • CHRND:cholinergic receptor nicotinic delta subunit [Gene - OMIM - HGNC]
  • CHRNG:cholinergic receptor nicotinic gamma subunit [Gene - OMIM - HGNC]
  • C2orf72:chromosome 2 open reading frame 72 [Gene - HGNC]
  • C2orf83:chromosome 2 open reading frame 83 [Gene - HGNC]
  • COL4A3:collagen type IV alpha 3 chain [Gene - OMIM - HGNC]
  • COL4A4:collagen type IV alpha 4 chain [Gene - OMIM - HGNC]
  • DNER:delta/notch like EGF repeat containing [Gene - OMIM - HGNC]
  • DGKD:diacylglycerol kinase delta [Gene - OMIM - HGNC]
  • DAW1:dynein assembly factor with WD repeats 1 [Gene - OMIM - HGNC]
  • ECEL1:endothelin converting enzyme like 1 [Gene - OMIM - HGNC]
  • EIF4E2:eukaryotic translation initiation factor 4E family member 2 [Gene - OMIM - HGNC]
  • GBX2:gastrulation brain homeobox 2 [Gene - OMIM - HGNC]
  • IRS1:insulin receptor substrate 1 [Gene - OMIM - HGNC]
  • ITM2C:integral membrane protein 2C [Gene - OMIM - HGNC]
  • MROH2A:maestro heat like repeat family member 2A [Gene - HGNC]
  • MFF:mitochondrial fission factor [Gene - OMIM - HGNC]
  • NPPC:natriuretic peptide C [Gene - OMIM - HGNC]
  • NEU2:neuraminidase 2 [Gene - OMIM - HGNC]
  • NMUR1:neuromedin U receptor 1 [Gene - OMIM - HGNC]
  • NGEF:neuronal guanine nucleotide exchange factor [Gene - OMIM - HGNC]
  • NYAP2:neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [Gene - OMIM - HGNC]
  • NCL:nucleolin [Gene - OMIM - HGNC]
  • PDE6D:phosphodiesterase 6D [Gene - OMIM - HGNC]
  • PID1:phosphotyrosine interaction domain containing 1 [Gene - OMIM - HGNC]
  • KCNJ13:potassium inwardly rectifying channel subfamily J member 13 [Gene - OMIM - HGNC]
  • PSMD1:proteasome 26S subunit, non-ATPase 1 [Gene - OMIM - HGNC]
  • PTMA:prothymosin alpha [Gene - OMIM - HGNC]
  • RHBDD1:rhomboid domain containing 1 [Gene - OMIM - HGNC]
  • SNORC:secondary ossification center associated regulator of chondrocyte maturation [Gene - HGNC]
  • SPP2:secreted phosphoprotein 2 [Gene - OMIM - HGNC]
  • PRSS56:serine protease 56 [Gene - OMIM - HGNC]
  • SNORD20:small nucleolar RNA, C/D box 20 [Gene - OMIM - HGNC]
  • SNORD82:small nucleolar RNA, C/D box 82 [Gene - OMIM - HGNC]
  • SLC16A14:solute carrier family 16 member 14 [Gene - HGNC]
  • SLC19A3:solute carrier family 19 member 3 [Gene - OMIM - HGNC]
  • SPATA3:spermatogenesis associated 3 [Gene - OMIM - HGNC]
  • TEX44:testis expressed 44 [Gene - HGNC]
  • TRIP12:thyroid hormone receptor interactor 12 [Gene - OMIM - HGNC]
  • TIGD1:tigger transposable element derived 1 [Gene - OMIM - HGNC]
  • TRPM8:transient receptor potential cation channel subfamily M member 8 [Gene - OMIM - HGNC]
  • TM4SF20:transmembrane 4 L six family member 20 [Gene - OMIM - HGNC]
  • USP40:ubiquitin specific peptidase 40 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
2q36.2-37.3
Genomic location:
Chr2: 225995545 - 237594511 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 2q36.2-37.3(chr2:225995545-237594511)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
    SCV004230863Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Apr 20, 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, SCV004230863.1

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

    Description

    The gain of 2q36.2q37.3 involves several protein-coding genes. Larger duplications overlapping this interval have been described in individuals with variable features including craniofacial abnormalities, developmental delay, and skeletal anomalies (Elbracht 2009, Ponnala 2012, Suzuki 2022). There are no similar copy number gains spanning this region in the general populations of the Database of Genomic Variants. Based on gene content, this copy number variant (CNV) is classified as likely pathogenic. References: Elbracht et al., Am J Med Genet A. 2009 Nov;149A(11):2547-50. PMID: 19876899 Gavril et al., Genes (Basel). 2023 Feb 11;14(2):465. PMID: 36833393 Le et al., Am J Med Genet A. 2019 May;179(5):782-791. PMID: 30848064 Ponnala et al., Cytogenet Genome Res. 2012;136(3):229-34. PMID: 22398442 Spielmann et al., Am J Med Genet A. 2016 May;170A(5):1202-7. PMID: 26822876 Suzuki et al., Hum Genome Var. 2022 Nov 10;9(1):39. PMID: 36357380

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

    Last Updated: Feb 4, 2024