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GRCh37/hg19 15q26.1(chr15:89520451-93926491)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 14, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001827973.1

Allele description [Variation Report for GRCh37/hg19 15q26.1(chr15:89520451-93926491)x1]

GRCh37/hg19 15q26.1(chr15:89520451-93926491)x1

Genes:
  • ARPIN-AP3S2:ARPIN-AP3S2 readthrough [Gene - HGNC]
  • BLM:BLM RecQ like helicase [Gene - OMIM - HGNC]
  • CRTC3:CREB regulated transcription coactivator 3 [Gene - OMIM - HGNC]
  • POLG:DNA polymerase gamma, catalytic subunit [Gene - OMIM - 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]
  • RCCD1:RCC1 domain containing 1 [Gene - OMIM - HGNC]
  • RHCG:Rh family C glycoprotein [Gene - OMIM - HGNC]
  • ST8SIA2:ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2 [Gene - OMIM - HGNC]
  • TICRR:TOPBP1 interacting checkpoint and replication regulator [Gene - OMIM - HGNC]
  • VPS33B:VPS33B late endosome and lysosome associated [Gene - OMIM - HGNC]
  • WDR93:WD repeat domain 93 [Gene - OMIM - HGNC]
  • ABHD2:abhydrolase domain containing 2, acylglycerol lipase [Gene - OMIM - HGNC]
  • ARPIN:actin related protein 2/3 complex inhibitor [Gene - OMIM - HGNC]
  • AP3S2:adaptor related protein complex 3 subunit sigma 2 [Gene - OMIM - HGNC]
  • ANPEP:alanyl aminopeptidase, membrane [Gene - OMIM - HGNC]
  • CIB1:calcium and integrin binding 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]
  • FURIN:furin, paired basic amino acid cleaving enzyme [Gene - OMIM - HGNC]
  • IDH2:isocitrate dehydrogenase (NADP(+)) 2 [Gene - OMIM - HGNC]
  • KIF7:kinesin family member 7 [Gene - OMIM - HGNC]
  • LINC00928:long intergenic non-protein coding RNA 928 [Gene - HGNC]
  • MAN2A2:mannosidase alpha class 2A member 2 [Gene - OMIM - HGNC]
  • MESP1:mesoderm posterior bHLH transcription factor 1 [Gene - OMIM - HGNC]
  • MESP2:mesoderm posterior bHLH transcription factor 2 [Gene - OMIM - HGNC]
  • MIR9-3:microRNA 9-3 [Gene - OMIM - HGNC]
  • NGRN:neugrin, neurite outgrowth associated [Gene - OMIM - HGNC]
  • PLIN1:perilipin 1 [Gene - OMIM - HGNC]
  • PEX11A:peroxisomal biogenesis factor 11 alpha [Gene - OMIM - HGNC]
  • PRC1:protein regulator of cytokinesis 1 [Gene - OMIM - HGNC]
  • RGMA:repulsive guidance molecule BMP co-receptor a [Gene - OMIM - HGNC]
  • RLBP1:retinaldehyde binding protein 1 [Gene - OMIM - HGNC]
  • SEMA4B:semaphorin 4B [Gene - OMIM - HGNC]
  • SLCO3A1:solute carrier organic anion transporter family member 3A1 [Gene - OMIM - HGNC]
  • SV2B:synaptic vesicle glycoprotein 2B [Gene - OMIM - HGNC]
  • UNC45A:unc-45 myosin chaperone A [Gene - OMIM - HGNC]
  • ZNF710:zinc finger protein 710 [Gene - HGNC]
  • ZNF774:zinc finger protein 774 [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
15q26.1
Genomic location:
Chr15: 89520451 - 93926491 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 15q26.1(chr15:89520451-93926491)x1
HGVS:
NC_000015.9:g.(?_89520451)_(93926491_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002096741Quest Diagnostics Nichols Institute San Juan Capistrano
no assertion criteria provided
Pathogenic
(Sep 14, 2020)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002096741.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This interstitial deletion of 15q26.1 involves multiple OMIM genes and is expected to cause phenotypic and/or developmental abnormalities. This locus falls within a much larger chromosomal region that is associated with the 15q26-qter deletion syndrome (OMIM 612626). Several similar or smaller deletions, mostly de novo, within 15q26.1 or 15q26.1-26.2 have been reported in individuals with a spectrum of phenotypes including epilepsy, intellectual disability, facial dysmorphism, minor physical anomalies, developmental delay, and/or speech delay (Veredice et al., Epilepsia. 2009 Jul;50(7):1810-5. PMID: 19486360; Dhamija et al., Pediatr Neurol. 2011 Jul;45(1):60-2. PMID: 21723464; Li et al., Am J Med Genet A. 2008 Feb 1;146A(3):368-75. PMID: 18203177). RGMA (OMIM 607362) and ST8SIA2 (OMIM 602546) at 15q26.1 have been suggested as candidate genes for the seizure phenotype. Additionally, haploinsufficiency, via loss-of-function sequence variants of CHD2 is associated with childhood-onset epileptic encephalopathy (OMIM 615369). This large deletion also includes other OMIM genes that are associated with autosomal dominant phenotypes: POLG (OMIM 157640), and RLBP1 (OMIM 136880).

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

Last Updated: Mar 26, 2023