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GRCh37/hg19 15q26.1-26.3(chr15:92335751-102399741)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 20, 2019
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:
RCV001537887.4

Allele description [Variation Report for GRCh37/hg19 15q26.1-26.3(chr15:92335751-102399741)x1]

GRCh37/hg19 15q26.1-26.3(chr15:92335751-102399741)x1

Genes:
  • ADAMTS17:ADAM metallopeptidase with thrombospondin type 1 motif 17 [Gene - OMIM - HGNC]
  • LYSMD4:LysM domain containing 4 [Gene - HGNC]
  • ST8SIA2:ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2 [Gene - OMIM - HGNC]
  • TM2D3:TM2 domain containing 3 [Gene - OMIM - HGNC]
  • ALDH1A3:aldehyde dehydrogenase 1 family member A3 [Gene - OMIM - HGNC]
  • ASB7:ankyrin repeat and SOCS box containing 7 [Gene - OMIM - HGNC]
  • ARRDC4:arrestin domain containing 4 [Gene - OMIM - HGNC]
  • CERS3:ceramide synthase 3 [Gene - OMIM - HGNC]
  • CHSY1:chondroitin sulfate synthase 1 [Gene - OMIM - HGNC]
  • CHD2:chromodomain helicase DNA binding protein 2 [Gene - OMIM - HGNC]
  • C15orf32:chromosome 15 putative open reading frame 32 [Gene - HGNC]
  • FAM174B:family with sequence similarity 174 member B [Gene - HGNC]
  • IGF1R:insulin like growth factor 1 receptor [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]
  • MCTP2:multiple C2 and transmembrane domain containing 2 [Gene - OMIM - HGNC]
  • MEF2A:myocyte enhancer factor 2A [Gene - OMIM - HGNC]
  • NR2F2:nuclear receptor subfamily 2 group F member 2 [Gene - OMIM - HGNC]
  • OR4F15:olfactory receptor family 4 subfamily F member 15 [Gene - HGNC]
  • OR4F6:olfactory receptor family 4 subfamily F member 6 [Gene - HGNC]
  • PCSK6:proprotein convertase subtilisin/kexin type 6 [Gene - OMIM - HGNC]
  • PGPEP1L:pyroglutamyl-peptidase I like [Gene - HGNC]
  • RGMA:repulsive guidance molecule BMP co-receptor a [Gene - OMIM - HGNC]
  • SELENOS:selenoprotein S [Gene - OMIM - HGNC]
  • SNRPA1:small nuclear ribonucleoprotein polypeptide A' [Gene - OMIM - HGNC]
  • SLCO3A1:solute carrier organic anion transporter family member 3A1 [Gene - OMIM - HGNC]
  • SPATA8:spermatogenesis associated 8 [Gene - OMIM - HGNC]
  • SYNM:synemin [Gene - OMIM - HGNC]
  • TTC23:tetratricopeptide repeat domain 23 [Gene - HGNC]
  • TARS3:threonyl-tRNA synthetase 3 [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
15q26.1-26.3
Genomic location:
Chr15: 92335751 - 102399741 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 15q26.1-26.3(chr15:92335751-102399741)x1
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
    SCV001754815Illumina Laboratory Services, Illumina
    criteria provided, single submitter

    (ICSL CNVClassificationCriteria Jul2020Prior)    		Pathogenic
    (Feb 20, 2019)     		unknownclinical testing

    PubMed (7)
    [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

    Identification of chromosome 15q26 terminal deletion with telomere sequences and its bearing on genotype-phenotype analysis.

    Dateki S, Fukami M, Tanaka Y, Sasaki G, Moriuchi H, Ogata T.

    Endocr J. 2011;58(3):155-9. Epub 2011 Jan 14.

    PubMed [citation]
    PMID:
    21242650

    Short stature due to 15q26 microdeletion involving IGF1R: report of an additional case and review of the literature.

    Rudaks LI, Nicholl JK, Bratkovic D, Barnett CP.

    Am J Med Genet A. 2011 Dec;155A(12):3139-43. doi: 10.1002/ajmg.a.34310. Epub 2011 Nov 7. Review. No abstract available.

    PubMed [citation]
    PMID:
    22065603
    See all PubMed Citations (7)

    Details of each submission

    From Illumina Laboratory Services, Illumina, SCV001754815.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedclinical testing PubMed (7)

    Description

    This CNV is a 10 Mb deletion of 15q26.1-q26.3, on chromosome 15, (seq[GRCh37]del(15)(q26.1q26.3); chr15:g.92335751-102399741del), found in a de novo state. This CNV constitutes a loss encompassing at least 70 genes and overlaps the 15q26 terminal deletion syndrome. The loss includes deletion of the IGF1R gene, which has been proposed as a candidate gene for several of the phenotypes associated with terminal deletions of 15q26 (O'Riordan et al. 2016). Growth hormone therapy in individuals affected with growth hormone resistance due to terminal 15q26 deletion has resulted in a moderate to dramatic response (Ho et al. 2015; Mahmoud et al. 2017). This CNV has not been reported in controls. Based on the collective 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