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GRCh37/hg19 2p25.3-22.3(chr2:706460-35523639)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 15, 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:
RCV002473946.1

Allele description [Variation Report for GRCh37/hg19 2p25.3-22.3(chr2:706460-35523639)x3]

GRCh37/hg19 2p25.3-22.3(chr2:706460-35523639)x3

Genes:
  • NT5C1B:5'-nucleotidase, cytosolic IB [Gene - OMIM - HGNC]
  • ADAM17:ADAM metallopeptidase domain 17 [Gene - OMIM - HGNC]
  • AGBL5:AGBL carboxypeptidase 5 [Gene - OMIM - HGNC]
  • ALK:ALK receptor tyrosine kinase [Gene - OMIM - HGNC]
  • ASXL2:ASXL transcriptional regulator 2 [Gene - OMIM - HGNC]
  • ATP6V1C2:ATPase H+ transporting V1 subunit C2 [Gene - OMIM - HGNC]
  • ATAD2B:ATPase family AAA domain containing 2B [Gene - OMIM - HGNC]
  • ASAP2:ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 [Gene - OMIM - HGNC]
  • BABAM2:BRISC and BRCA1 A complex member 2 [Gene - OMIM - HGNC]
  • CLIP4:CAP-Gly domain containing linker protein family member 4 [Gene - HGNC]
  • CYRIA:CYFIP related Rac1 interactor A [Gene - HGNC]
  • DDX1:DEAD-box helicase 1 [Gene - OMIM - HGNC]
  • DNMT3A:DNA methyltransferase 3 alpha [Gene - OMIM - HGNC]
  • DNAJC27:DnaJ heat shock protein family (Hsp40) member C27 [Gene - OMIM - HGNC]
  • DNAJC5G:DnaJ heat shock protein family (Hsp40) member C5 gamma [Gene - OMIM - HGNC]
  • E2F6:E2F transcription factor 6 [Gene - OMIM - HGNC]
  • EIPR1:EARP complex and GARP complex interacting protein 1 [Gene - OMIM - HGNC]
  • EFR3B:EFR3 homolog B [Gene - OMIM - HGNC]
  • EHD3:EH domain containing 3 [Gene - OMIM - HGNC]
  • FKBP1B:FKBP prolyl isomerase 1B [Gene - OMIM - HGNC]
  • FOSL2:FOS like 2, AP-1 transcription factor subunit [Gene - OMIM - HGNC]
  • GEN1:GEN1 Holliday junction 5' flap endonuclease [Gene - OMIM - HGNC]
  • GPN1:GPN-loop GTPase 1 [Gene - OMIM - HGNC]
  • GAREM2:GRB2 associated regulator of MAPK1 subtype 2 [Gene - OMIM - HGNC]
  • HS1BP3:HCLS1 binding protein 3 [Gene - OMIM - HGNC]
  • KLF11:KLF transcription factor 11 [Gene - OMIM - HGNC]
  • LBH:LBH regulator of WNT signaling pathway [Gene - OMIM - HGNC]
  • LRATD1:LRAT domain containing 1 [Gene - OMIM - HGNC]
  • MFSD2B:MFSD2 lysolipid transporter B, sphingolipid [Gene - OMIM - HGNC]
  • MYCNOS:MYCN opposite strand [Gene - OMIM - HGNC]
  • MYCN:MYCN proto-oncogene, bHLH transcription factor [Gene - OMIM - HGNC]
  • NBAS:NBAS subunit of NRZ tethering complex [Gene - OMIM - HGNC]
  • NLRC4:NLR family CARD domain containing 4 [Gene - OMIM - HGNC]
  • NT5C1B-RDH14:NT5C1B-RDH14 readthrough [Gene - HGNC]
  • RAB10:RAB10, member RAS oncogene family [Gene - OMIM - HGNC]
  • RAD51AP2:RAD51 associated protein 2 [Gene - HGNC]
  • RASGRP3:RAS guanyl releasing protein 3 [Gene - OMIM - HGNC]
  • ROCK2:Rho associated coiled-coil containing protein kinase 2 [Gene - OMIM - HGNC]
  • SUPT7L:SPT7 like, STAGA complex subunit gamma [Gene - OMIM - HGNC]
  • SOX11:SRY-box transcription factor 11 [Gene - OMIM - HGNC]
  • TAF1B:TATA-box binding protein associated factor, RNA polymerase I subunit B [Gene - OMIM - HGNC]
  • TOGARAM2:TOG array regulator of axonemal microtubules 2 [Gene - HGNC]
  • UBXN2A:UBX domain protein 2A [Gene - HGNC]
  • WDCP:WD repeat and coiled coil containing [Gene - OMIM - HGNC]
  • WDR35:WD repeat domain 35 [Gene - OMIM - HGNC]
  • WDR43:WD repeat domain 43 [Gene - OMIM - HGNC]
  • YIPF4:Yip1 domain family member 4 [Gene - OMIM - HGNC]
  • ABHD1:abhydrolase domain containing 1 [Gene - OMIM - HGNC]
  • ADI1:acireductone dioxygenase 1 [Gene - OMIM - HGNC]
  • ADCY3:adenylate cyclase 3 [Gene - OMIM - HGNC]
  • ADGRF3:adhesion G protein-coupled receptor F3 [Gene - HGNC]
  • ATRAID:all-trans retinoic acid induced differentiation factor [Gene - OMIM - HGNC]
  • ALLC:allantoicase [Gene - OMIM - HGNC]
  • APOB:apolipoprotein B [Gene - OMIM - HGNC]
  • BIRC6:baculoviral IAP repeat containing 6 [Gene - OMIM - HGNC]
  • CIB4:calcium and integrin binding family member 4 [Gene - OMIM - HGNC]
  • CAPN13:calpain 13 [Gene - OMIM - HGNC]
  • CAPN14:calpain 14 [Gene - OMIM - HGNC]
  • CAD:carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase [Gene - OMIM - HGNC]
  • CGREF1:cell growth regulator with EF-hand domain 1 [Gene - OMIM - HGNC]
  • CENPA:centromere protein A [Gene - OMIM - HGNC]
  • CENPO:centromere protein O [Gene - OMIM - HGNC]
  • C2orf16:chromosome 2 open reading frame 16 [Gene - HGNC]
  • C2orf48:chromosome 2 open reading frame 48 [Gene - HGNC]
  • C2orf50:chromosome 2 open reading frame 50 [Gene - HGNC]
  • CPSF3:cleavage and polyadenylation specific factor 3 [Gene - OMIM - HGNC]
  • CCDC121:coiled-coil domain containing 121 [Gene - HGNC]
  • COLEC11:collectin subfamily member 11 [Gene - OMIM - HGNC]
  • CYS1:cystin 1 [Gene - OMIM - HGNC]
  • CMPK2:cytidine/uridine monophosphate kinase 2 [Gene - OMIM - HGNC]
  • DPYSL5:dihydropyrimidinase like 5 [Gene - OMIM - HGNC]
  • DCDC2C:doublecortin domain containing 2C [Gene - HGNC]
  • DPY30:dpy-30 histone methyltransferase complex regulatory subunit [Gene - OMIM - HGNC]
  • DRC1:dynein regulatory complex subunit 1 [Gene - OMIM - HGNC]
  • DTNB:dystrobrevin beta [Gene - OMIM - HGNC]
  • EMILIN1:elastin microfibril interfacer 1 [Gene - OMIM - HGNC]
  • EIF2B4:eukaryotic translation initiation factor 2B subunit delta [Gene - OMIM - HGNC]
  • FAM166C:family with sequence similarity 166 member C [Gene - HGNC]
  • FAM228A:family with sequence similarity 228 member A [Gene - HGNC]
  • FAM228B:family with sequence similarity 228 member B [Gene - HGNC]
  • FAM98A:family with sequence similarity 98 member A [Gene - HGNC]
  • FNDC4:fibronectin type III domain containing 4 [Gene - OMIM - HGNC]
  • GTF3C2:general transcription factor IIIC subunit 2 [Gene - OMIM - HGNC]
  • GCKR:glucokinase regulator [Gene - OMIM - HGNC]
  • GRHL1:grainyhead like transcription factor 1 [Gene - OMIM - HGNC]
  • GDF7:growth differentiation factor 7 [Gene - OMIM - HGNC]
  • GREB1:growth regulating estrogen receptor binding 1 [Gene - OMIM - HGNC]
  • HPCAL1:hippocalcin like 1 [Gene - OMIM - HGNC]
  • HADHA:hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha [Gene - OMIM - HGNC]
  • HADHB:hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit beta [Gene - OMIM - HGNC]
  • ID2:inhibitor of DNA binding 2 [Gene - OMIM - HGNC]
  • ITGB1BP1:integrin subunit beta 1 binding protein 1 [Gene - OMIM - HGNC]
  • ITSN2:intersectin 2 [Gene - OMIM - HGNC]
  • IFT172:intraflagellar transport 172 [Gene - OMIM - HGNC]
  • IAH1:isoamyl acetate hydrolyzing esterase 1 (putative) [Gene - HGNC]
  • KLHL29:kelch like family member 29 [Gene - HGNC]
  • KRTCAP3:keratinocyte associated protein 3 [Gene - OMIM - HGNC]
  • KHK:ketohexokinase [Gene - OMIM - HGNC]
  • KIDINS220:kinase D interacting substrate 220 [Gene - OMIM - HGNC]
  • KIF3C:kinesin family member 3C [Gene - OMIM - HGNC]
  • LTBP1:latent transforming growth factor beta binding protein 1 [Gene - OMIM - HGNC]
  • LDAH:lipid droplet associated hydrolase [Gene - OMIM - HGNC]
  • LPIN1:lipin 1 [Gene - OMIM - HGNC]
  • LINC00570:long intergenic non-protein coding RNA 570 [Gene - HGNC]
  • LCLAT1:lysocardiolipin acyltransferase 1 [Gene - OMIM - HGNC]
  • LAPTM4A:lysosomal protein transmembrane 4 alpha [Gene - OMIM - HGNC]
  • MATN3:matrilin 3 [Gene - OMIM - HGNC]
  • MEMO1:mediator of cell motility 1 [Gene - OMIM - HGNC]
  • MBOAT2:membrane bound O-acyltransferase domain containing 2 [Gene - OMIM - HGNC]
  • MSGN1:mesogenin 1 [Gene - OMIM - HGNC]
  • MAPRE3:microtubule associated protein RP/EB family member 3 [Gene - OMIM - HGNC]
  • MPV17:mitochondrial inner membrane protein MPV17 [Gene - OMIM - HGNC]
  • MRPL33:mitochondrial ribosomal protein L33 [Gene - OMIM - HGNC]
  • MYT1L:myelin transcription factor 1 like [Gene - OMIM - HGNC]
  • NTSR2:neurotensin receptor 2 [Gene - OMIM - HGNC]
  • NRBP1:nuclear receptor binding protein 1 [Gene - OMIM - HGNC]
  • NCOA1:nuclear receptor coactivator 1 [Gene - OMIM - HGNC]
  • NOL10:nucleolar protein 10 [Gene - OMIM - HGNC]
  • OSR1:odd-skipped related transcription factor 1 [Gene - OMIM - HGNC]
  • OST4:oligosaccharyltransferase complex subunit 4, non-catalytic [Gene - OMIM - HGNC]
  • ODC1:ornithine decarboxylase 1 [Gene - OMIM - HGNC]
  • OTOF:otoferlin [Gene - OMIM - HGNC]
  • PTRHD1:peptidyl-tRNA hydrolase domain containing 1 [Gene - OMIM - HGNC]
  • PXDN:peroxidasin [Gene - OMIM - HGNC]
  • PLB1:phospholipase B1 [Gene - OMIM - HGNC]
  • PCARE:photoreceptor cilium actin regulator [Gene - OMIM - HGNC]
  • GALNT14:polypeptide N-acetylgalactosaminyltransferase 14 [Gene - OMIM - HGNC]
  • KCNK3:potassium two pore domain channel subfamily K member 3 [Gene - OMIM - HGNC]
  • KCNF1:potassium voltage-gated channel modifier subfamily F member 1 [Gene - OMIM - HGNC]
  • KCNS3:potassium voltage-gated channel modifier subfamily S member 3 [Gene - OMIM - HGNC]
  • PFN4:profilin family member 4 [Gene - OMIM - HGNC]
  • PREB:prolactin regulatory element binding [Gene - OMIM - HGNC]
  • PRR30:proline rich 30 [Gene - HGNC]
  • POMC:proopiomelanocortin [Gene - OMIM - HGNC]
  • PDIA6:protein disulfide isomerase family A member 6 [Gene - OMIM - HGNC]
  • PPP1CB:protein phosphatase 1 catalytic subunit beta [Gene - OMIM - HGNC]
  • PPM1G:protein phosphatase, Mg2+/Mn2+ dependent 1G [Gene - OMIM - HGNC]
  • PUM2:pumilio RNA binding family member 2 [Gene - OMIM - HGNC]
  • RSAD2:radical S-adenosyl methionine domain containing 2 [Gene - OMIM - HGNC]
  • RHOB:ras homolog family member B [Gene - OMIM - HGNC]
  • RDH14:retinol dehydrogenase 14 [Gene - OMIM - HGNC]
  • RBKS:ribokinase [Gene - OMIM - HGNC]
  • RNASEH1:ribonuclease H1 [Gene - OMIM - HGNC]
  • RRM2:ribonucleotide reductase regulatory subunit M2 [Gene - OMIM - HGNC]
  • RPS7:ribosomal protein S7 [Gene - OMIM - HGNC]
  • RNF144A:ring finger protein 144A [Gene - OMIM - HGNC]
  • SELENOI:selenoprotein I [Gene - OMIM - HGNC]
  • SLC30A3:solute carrier family 30 member 3 [Gene - OMIM - HGNC]
  • SLC30A6:solute carrier family 30 member 6 [Gene - OMIM - HGNC]
  • SLC35F6:solute carrier family 35 member F6 [Gene - OMIM - HGNC]
  • SLC4A1AP:solute carrier family 4 member 1 adaptor protein [Gene - OMIM - HGNC]
  • SLC5A6:solute carrier family 5 member 6 [Gene - OMIM - HGNC]
  • SLC66A3:solute carrier family 66 member 3 [Gene - HGNC]
  • SNX17:sorting nexin 17 [Gene - OMIM - HGNC]
  • SPAST:spastin [Gene - OMIM - HGNC]
  • SPDYA:speedy/RINGO cell cycle regulator family member A [Gene - OMIM - HGNC]
  • SF3B6:splicing factor 3b subunit 6 [Gene - OMIM - HGNC]
  • SRD5A2:steroid 5 alpha-reductase 2 [Gene - OMIM - HGNC]
  • SMC6:structural maintenance of chromosomes 6 [Gene - OMIM - HGNC]
  • SDC1:syndecan 1 [Gene - OMIM - HGNC]
  • SNTG2:syntrophin gamma 2 [Gene - OMIM - HGNC]
  • TRMT61B:tRNA methyltransferase 61B [Gene - OMIM - HGNC]
  • TTC27:tetratricopeptide repeat domain 27 [Gene - HGNC]
  • TTC32:tetratricopeptide repeat domain 32 [Gene - HGNC]
  • TPO:thyroid peroxidase [Gene - OMIM - HGNC]
  • TRAPPC12:trafficking protein particle complex subunit 12 [Gene - OMIM - HGNC]
  • TCF23:transcription factor 23 [Gene - OMIM - HGNC]
  • TMEM214:transmembrane protein 214 [Gene - OMIM - HGNC]
  • TRIB2:tribbles pseudokinase 2 [Gene - OMIM - HGNC]
  • TRIM54:tripartite motif containing 54 [Gene - OMIM - HGNC]
  • TDRD15:tudor domain containing 15 [Gene - HGNC]
  • TP53I3:tumor protein p53 inducible protein 3 [Gene - OMIM - HGNC]
  • YWHAQ:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta [Gene - OMIM - HGNC]
  • UCN:urocortin [Gene - OMIM - HGNC]
  • VSNL1:visinin like 1 [Gene - OMIM - HGNC]
  • XDH:xanthine dehydrogenase [Gene - OMIM - HGNC]
  • YPEL5:yippee like 5 [Gene - OMIM - HGNC]
  • ZNF512:zinc finger protein 512 [Gene - HGNC]
  • ZNF513:zinc finger protein 513 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
2p25.3-22.3
Genomic location:
Chr2: 706460 - 35523639 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 2p25.3-22.3(chr2:706460-35523639)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
    SCV002773812Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Apr 15, 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, SCV002773812.1

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

    Description

    This large gain involves numerous protein-coding genes, including multiple associated with autosomal dominant disorders: MYT1L (OMIM 613084), RPS7 (OMIM 603658), SOX11 (OMIM 600898), KIDINS220 (OMIM 615759), ODC1 (OMIM 165640), MYCN (OMIM 164840), MATN3 (OMIM 602109), APOB (OMIM 107730), POMC (OMIM 176830), DNMT3A (OMIM 602769), ASXL2 (OMIM 612991), KCNK3 (OMIM 603220), DPYSL5 (OMIM 608383), PPP1CB (OMIM 600590), SPAST (OMIM 604277), and NLRC4 (OMIM 606831). Partial trisomy 2p, including pure duplications similar in size and gene content to the current interval, has been described in numerous patients with variable clinical features, including dysmorphic features, psychomotor delay, cardiac and pulmonary anomalies, growth failure, neural tube defects and increased risk for neuroblastoma and renal tumors (Al-Saffar 2000, Fievet 2013, Lurie 2014, Martinez-Juarez 2014, Micale 2016, Schwab 2004, Van Mater 2013). There are no similar copy number gains of this region in the general populations of the Database of Genomic Variants. Thus, based on gene content and current medical literature, the classification of this copy number variant (CNV) is pathogenic. References Al-Saffar et al., Am J Med Genet. 2000 Oct 23;94(5):428-32. PMID: 11050631 Fievet et al., Eur J Med Genet. 2013 Dec;56(12):643-7. PMID: 24161495. Lurie et al., Cytogenet Genome Res. 2014;144(1):28-30. PMID: 25322981. Martinez-Juarez et al., Cytogenet Genome Res. 2014;142(4):249-54. PMID: 24751616. Micale et al., Eur J Med Genet. 2016 Dec;59(12):618-623. PMID: 27794475. Schwab et al., Cancer Lett. 2004 Feb 20;204(2):179-87. PMID: 15013217. Van Mater et al., Am J Med Genet A. 2013 Mar;161A(3):605-10. PMID: 23401364.

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

    Last Updated: Mar 26, 2023