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GRCh37/hg19 15q24.3-26.3(chr15:77512817-102035027)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 9, 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:
RCV002475797.1

Allele description [Variation Report for GRCh37/hg19 15q24.3-26.3(chr15:77512817-102035027)x3]

GRCh37/hg19 15q24.3-26.3(chr15:77512817-102035027)x3

Genes:
  • AKAP13:A-kinase anchoring protein 13 [Gene - OMIM - HGNC]
  • ADAMTS17:ADAM metallopeptidase with thrombospondin type 1 motif 17 [Gene - OMIM - HGNC]
  • ADAMTS7:ADAM metallopeptidase with thrombospondin type 1 motif 7 [Gene - OMIM - HGNC]
  • ADAMTSL3:ADAMTS like 3 [Gene - OMIM - HGNC]
  • AGBL1:AGBL carboxypeptidase 1 [Gene - OMIM - HGNC]
  • ARPIN-AP3S2:ARPIN-AP3S2 readthrough [Gene - HGNC]
  • BCL2A1:BCL2 related protein A1 [Gene - OMIM - HGNC]
  • BLM:BLM RecQ like helicase [Gene - OMIM - HGNC]
  • BTBD1:BTB domain containing 1 [Gene - OMIM - HGNC]
  • CRTC3:CREB regulated transcription coactivator 3 [Gene - OMIM - HGNC]
  • DET1:DET1 partner of COP1 E3 ubiquitin ligase [Gene - OMIM - HGNC]
  • POLG:DNA polymerase gamma, catalytic subunit [Gene - OMIM - HGNC]
  • DNAJA4:DnaJ heat shock protein family (Hsp40) member A4 [Gene - HGNC]
  • FANCI:FA complementation group I [Gene - OMIM - HGNC]
  • FES:FES proto-oncogene, tyrosine kinase [Gene - OMIM - HGNC]
  • GDPGP1:GDP-D-glucose phosphorylase 1 [Gene - OMIM - HGNC]
  • HDDC3:HD domain containing 3 [Gene - HGNC]
  • IQGAP1:IQ motif containing GTPase activating protein 1 [Gene - OMIM - HGNC]
  • LYSMD4:LysM domain containing 4 [Gene - HGNC]
  • RCCD1:RCC1 domain containing 1 [Gene - OMIM - HGNC]
  • RAMAC:RNA guanine-7 methyltransferase activating subunit [Gene - OMIM - HGNC]
  • RASGRF1:Ras protein specific guanine nucleotide releasing factor 1 [Gene - OMIM - HGNC]
  • RHCG:Rh family C glycoprotein [Gene - OMIM - HGNC]
  • SEC11A:SEC11 homolog A, signal peptidase complex subunit [Gene - OMIM - HGNC]
  • SH2D7:SH2 domain containing 7 [Gene - HGNC]
  • SH3GL3:SH3 domain containing GRB2 like 3, endophilin A3 [Gene - OMIM - HGNC]
  • SKIC8:SKI8 subunit of superkiller complex [Gene - OMIM - HGNC]
  • ST20-MTHFS:ST20-MTHFS readthrough [Gene - HGNC]
  • ST8SIA2:ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2 [Gene - OMIM - HGNC]
  • STARD5:StAR related lipid transfer domain containing 5 [Gene - OMIM - HGNC]
  • TBC1D2B:TBC1 domain family member 2B [Gene - OMIM - HGNC]
  • TICRR:TOPBP1 interacting checkpoint and replication regulator [Gene - OMIM - HGNC]
  • VPS33B:VPS33B late endosome and lysosome associated [Gene - OMIM - HGNC]
  • WHAMM:WASP homolog associated with actin, golgi membranes and microtubules [Gene - OMIM - HGNC]
  • WDR73:WD repeat domain 73 [Gene - OMIM - HGNC]
  • WDR93:WD repeat domain 93 [Gene - OMIM - HGNC]
  • ABHD17C:abhydrolase domain containing 17C, depalmitoylase [Gene - OMIM - HGNC]
  • ABHD2:abhydrolase domain containing 2, acylglycerol lipase [Gene - OMIM - HGNC]
  • ARPIN:actin related protein 2/3 complex inhibitor [Gene - OMIM - HGNC]
  • ACSBG1:acyl-CoA synthetase bubblegum family member 1 [Gene - OMIM - HGNC]
  • AP3B2:adaptor related protein complex 3 subunit beta 2 [Gene - OMIM - HGNC]
  • AP3S2:adaptor related protein complex 3 subunit sigma 2 [Gene - OMIM - HGNC]
  • ACAN:aggrecan [Gene - OMIM - HGNC]
  • ANPEP:alanyl aminopeptidase, membrane [Gene - OMIM - HGNC]
  • ALDH1A3:aldehyde dehydrogenase 1 family member A3 [Gene - OMIM - HGNC]
  • ALPK3:alpha kinase 3 [Gene - OMIM - HGNC]
  • ASB7:ankyrin repeat and SOCS box containing 7 [Gene - OMIM - HGNC]
  • ANKRD34C:ankyrin repeat domain 34C [Gene - HGNC]
  • AEN:apoptosis enhancing nuclease [Gene - OMIM - HGNC]
  • ARRDC4:arrestin domain containing 4 [Gene - OMIM - HGNC]
  • ARNT2:aryl hydrocarbon receptor nuclear translocator 2 [Gene - OMIM - HGNC]
  • BNC1:basonuclin 1 [Gene - OMIM - HGNC]
  • CIB1:calcium and integrin binding 1 [Gene - OMIM - HGNC]
  • CIB2:calcium and integrin binding family member 2 [Gene - OMIM - HGNC]
  • CTSH:cathepsin H [Gene - OMIM - HGNC]
  • CEMIP:cell migration inducing hyaluronidase 1 [Gene - OMIM - HGNC]
  • CRABP1:cellular retinoic acid binding protein 1 [Gene - OMIM - HGNC]
  • CERS3:ceramide synthase 3 [Gene - OMIM - HGNC]
  • CHRNA3:cholinergic receptor nicotinic alpha 3 subunit [Gene - OMIM - HGNC]
  • CHRNA5:cholinergic receptor nicotinic alpha 5 subunit [Gene - OMIM - HGNC]
  • CHRNB4:cholinergic receptor nicotinic beta 4 subunit [Gene - OMIM - HGNC]
  • CHSY1:chondroitin sulfate synthase 1 [Gene - OMIM - HGNC]
  • CHD2:chromodomain helicase DNA binding protein 2 [Gene - OMIM - HGNC]
  • C15orf40:chromosome 15 open reading frame 40 [Gene - HGNC]
  • C15orf32:chromosome 15 putative open reading frame 32 [Gene - HGNC]
  • CFAP161:cilia and flagella associated protein 161 [Gene - HGNC]
  • CPEB1:cytoplasmic polyadenylation element binding protein 1 [Gene - OMIM - HGNC]
  • EFL1:elongation factor like GTPase 1 [Gene - OMIM - HGNC]
  • FAM174B:family with sequence similarity 174 member B [Gene - HGNC]
  • FSD2:fibronectin type III and SPRY domain containing 2 [Gene - HGNC]
  • FAH:fumarylacetoacetate hydrolase [Gene - OMIM - HGNC]
  • FURIN:furin, paired basic amino acid cleaving enzyme [Gene - OMIM - HGNC]
  • HMG20A:high mobility group 20A [Gene - OMIM - HGNC]
  • HOMER2:homer scaffold protein 2 [Gene - OMIM - HGNC]
  • HAPLN3:hyaluronan and proteoglycan link protein 3 [Gene - HGNC]
  • HYKK:hydroxylysine kinase [Gene - OMIM - HGNC]
  • IGF1R:insulin like growth factor 1 receptor [Gene - OMIM - HGNC]
  • ISG20:interferon stimulated exonuclease gene 20 [Gene - OMIM - HGNC]
  • IL16:interleukin 16 [Gene - OMIM - HGNC]
  • IREB2:iron responsive element binding protein 2 [Gene - OMIM - HGNC]
  • IDH3A:isocitrate dehydrogenase (NAD(+)) 3 catalytic subunit alpha [Gene - OMIM - HGNC]
  • IDH2:isocitrate dehydrogenase (NADP(+)) 2 [Gene - OMIM - HGNC]
  • KLHL25:kelch like family member 25 [Gene - OMIM - HGNC]
  • KIF7:kinesin family member 7 [Gene - OMIM - HGNC]
  • LINGO1:leucine rich repeat and Ig domain containing 1 [Gene - OMIM - HGNC]
  • LRRC28:leucine rich repeat containing 28 [Gene - HGNC]
  • LRRK1:leucine rich repeat kinase 1 [Gene - OMIM - HGNC]
  • LINS1:lines homolog 1 [Gene - OMIM - HGNC]
  • LINC00928:long intergenic non-protein coding RNA 928 [Gene - HGNC]
  • MAN2A2:mannosidase alpha class 2A member 2 [Gene - OMIM - HGNC]
  • MINAR1:membrane integral NOTCH2 associated receptor 1 [Gene - OMIM - HGNC]
  • MESD:mesoderm development LRP chaperone [Gene - OMIM - HGNC]
  • MESP1:mesoderm posterior bHLH transcription factor 1 [Gene - OMIM - HGNC]
  • MESP2:mesoderm posterior bHLH transcription factor 2 [Gene - OMIM - HGNC]
  • MTHFS:methenyltetrahydrofolate synthetase [Gene - OMIM - HGNC]
  • MEX3B:mex-3 RNA binding family member B [Gene - OMIM - HGNC]
  • MIR184:microRNA 184 [Gene - OMIM - HGNC]
  • MIR9-3:microRNA 9-3 [Gene - OMIM - HGNC]
  • MFGE8:milk fat globule EGF and factor V/VIII domain containing [Gene - OMIM - HGNC]
  • MRPL46:mitochondrial ribosomal protein L46 [Gene - OMIM - HGNC]
  • MRPS11:mitochondrial ribosomal protein S11 [Gene - OMIM - HGNC]
  • MORF4L1:mortality factor 4 like 1 [Gene - OMIM - HGNC]
  • MCTP2:multiple C2 and transmembrane domain containing 2 [Gene - OMIM - HGNC]
  • MEF2A:myocyte enhancer factor 2A [Gene - OMIM - HGNC]
  • NGRN:neugrin, neurite outgrowth associated [Gene - OMIM - HGNC]
  • NMB:neuromedin B [Gene - OMIM - HGNC]
  • NTRK3:neurotrophic receptor tyrosine kinase 3 [Gene - OMIM - HGNC]
  • NR2F2:nuclear receptor subfamily 2 group F member 2 [Gene - OMIM - HGNC]
  • PLIN1:perilipin 1 [Gene - OMIM - HGNC]
  • PEX11A:peroxisomal biogenesis factor 11 alpha [Gene - OMIM - HGNC]
  • PDE8A:phosphodiesterase 8A [Gene - OMIM - HGNC]
  • PCSK6:proprotein convertase subtilisin/kexin type 6 [Gene - OMIM - HGNC]
  • PSMA4:proteasome 20S subunit alpha 4 [Gene - OMIM - HGNC]
  • PRC1:protein regulator of cytokinesis 1 [Gene - OMIM - HGNC]
  • PEAK1:pseudopodium enriched atypical kinase 1 [Gene - OMIM - HGNC]
  • PGPEP1L:pyroglutamyl-peptidase I like [Gene - HGNC]
  • RGMA:repulsive guidance molecule BMP co-receptor a [Gene - OMIM - HGNC]
  • RLBP1:retinaldehyde binding protein 1 [Gene - OMIM - HGNC]
  • RPS17:ribosomal protein S17 [Gene - OMIM - HGNC]
  • SELENOS:selenoprotein S [Gene - OMIM - HGNC]
  • SEMA4B:semaphorin 4B [Gene - OMIM - HGNC]
  • SCARNA15:small Cajal body-specific RNA 15 [Gene - OMIM - HGNC]
  • SNRPA1:small nuclear ribonucleoprotein polypeptide A' [Gene - OMIM - HGNC]
  • SLC28A1:solute carrier family 28 member 1 [Gene - OMIM - HGNC]
  • SLCO3A1:solute carrier organic anion transporter family member 3A1 [Gene - OMIM - HGNC]
  • SPATA8:spermatogenesis associated 8 [Gene - OMIM - HGNC]
  • SAXO2:stabilizer of axonemal microtubules 2 [Gene - HGNC]
  • ST20:suppressor of tumorigenicity 20 [Gene - HGNC]
  • SV2B:synaptic vesicle glycoprotein 2B [Gene - OMIM - HGNC]
  • SYNM:synemin [Gene - OMIM - HGNC]
  • TLNRD1:talin rod domain containing 1 [Gene - OMIM - HGNC]
  • TTC23:tetratricopeptide repeat domain 23 [Gene - HGNC]
  • TM6SF1:transmembrane 6 superfamily member 1 [Gene - OMIM - HGNC]
  • TMC3:transmembrane channel like 3 [Gene - OMIM - HGNC]
  • TMED3:transmembrane p24 trafficking protein 3 [Gene - HGNC]
  • UNC45A:unc-45 myosin chaperone A [Gene - OMIM - HGNC]
  • ZFAND6:zinc finger AN1-type containing 6 [Gene - OMIM - HGNC]
  • ZSCAN2:zinc finger and SCAN domain containing 2 [Gene - HGNC]
  • ZNF592:zinc finger protein 592 [Gene - OMIM - HGNC]
  • ZNF710:zinc finger protein 710 [Gene - HGNC]
  • ZNF774:zinc finger protein 774 [Gene - HGNC]
Variant type:
copy number gain
Cytogenetic location:
15q24.3-26.3
Genomic location:
Chr15: 77512817 - 102035027 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 15q24.3-26.3(chr15:77512817-102035027)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
    SCV002773385Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Nov 9, 2021)     		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.

    PubMed [citation]
    PMID:
    31690835
    PMCID:
    PMC7313390

    Details of each submission

    From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002773385.1

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

    Description

    The copy number gain of 15q24.3q26.3 involves multiple chromosomal bands and is expected to cause phenotypic and/or developmental abnormalities. It includes 13 genes associated with autosomal dominant disorders. Terminal duplications of 15q25q26 have been associated with a prenatal and postnatal overgrowth syndrome characterized by tall stature, renal abnormalities, variable intellectual disability, and craniofacial abnormalities including macrocephaly and craniosynostosis (Cannarella 2017, Gutierrez-Franco 2010, Kim 2011, O'Connor 2011, Zollino 1999). The genes IGF1R (OMIM 147370) or LRRK1 (OMIM 610986) have been proposed as candidate genes for the overgrowth phenotype, both of which are encompassed in the current gain interval (Leffler 2016, Tatton-Brown 2009, Roggenbuck 2004, Allen 1992). References: Zollino et al., Am J Med Genet. 1999 Dec 22;87(5):391-4. PMID:10594876. Cannarella et al., Endocr Connect. 2017 Oct;6(7):528-539. PMID:28899882. Gutierrez-Franco et al., Korean J Lab Med. 2010 Jun;30(3):318-24.PMID: 20603595. Kim et al., Korean J Pediatr. 2011 Jun;54(6):267-71. PMID: 21949522. O'Connor et al., Case Rep Genet. 2011:898706. PMID: 23074681.Leffler et al., Eur J Med Genet. 2016 Apr;59(4):257-62. PMID:26689622. Tatton-Brown K et al., Am J Med Genet A. 2009 Feb; 149A (2):147-54. PMID: 19133692. Roggenbuck et al., Am J Med Genet A. 2004 May 1;126A(4):398-402.PMID: 15098238. Allen et al., Am J Med Genet. 1992 Jul 1;43(4):688-92. PMID: 1621758.

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

    Last Updated: Mar 26, 2023