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GRCh37/hg19 15q14-15.1 chr15:34638237..42057083 complex variant AND Spindle cell sarcoma

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 27, 2018
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:
RCV000714282.1

Allele description [Variation Report for GRCh37/hg19 15q14-15.1 chr15:34638237..42057083 complex variant]

GRCh37/hg19 15q14-15.1 chr15:34638237..42057083 complex variant

Genes:
  • BUB1B:BUB1 mitotic checkpoint serine/threonine kinase B [Gene - OMIM - HGNC]
  • BMF:Bcl2 modifying factor [Gene - OMIM - HGNC]
  • CDIN1:CDAN1 interacting nuclease 1 [Gene - OMIM - HGNC]
  • CHAC1:ChaC glutathione specific gamma-glutamylcyclotransferase 1 [Gene - OMIM - HGNC]
  • DNAJC17:DnaJ heat shock protein family (Hsp40) member C17 [Gene - OMIM - HGNC]
  • GPR176:G protein-coupled receptor 176 [Gene - OMIM - HGNC]
  • GCHFR:GTP cyclohydrolase I feedback regulator [Gene - OMIM - HGNC]
  • INO80:INO80 complex ATPase subunit [Gene - OMIM - HGNC]
  • MGA:MAX dimerization protein MGA [Gene - OMIM - HGNC]
  • MEIS2:Meis homeobox 2 [Gene - OMIM - HGNC]
  • NDUFAF1:NADH:ubiquinone oxidoreductase complex assembly factor 1 [Gene - OMIM - HGNC]
  • NUTM1:NUT midline carcinoma family member 1 [Gene - OMIM - HGNC]
  • OIP5:Opa interacting protein 5 [Gene - OMIM - HGNC]
  • PAK6-AS1:PAK6 antisense RNA 1 [Gene - HGNC]
  • RAD51:RAD51 recombinase [Gene - OMIM - HGNC]
  • RASGRP1:RAS guanyl releasing protein 1 [Gene - OMIM - HGNC]
  • RPAP1:RNA polymerase II associated protein 1 [Gene - OMIM - HGNC]
  • RPUSD2:RNA pseudouridine synthase domain containing 2 [Gene - HGNC]
  • RTF1:RTF1 homolog, Paf1/RNA polymerase II complex component [Gene - OMIM - HGNC]
  • TYRO3:TYRO3 protein tyrosine kinase [Gene - OMIM - HGNC]
  • VPS18:VPS18 core subunit of CORVET and HOPS complexes [Gene - OMIM - HGNC]
  • ACTC1:actin alpha cardiac muscle 1 [Gene - OMIM - HGNC]
  • ANKRD63:ankyrin repeat domain 63 [Gene - HGNC]
  • AQR:aquarius intron-binding spliceosomal factor [Gene - OMIM - HGNC]
  • BAHD1:bromo adjacent homology domain containing 1 [Gene - OMIM - HGNC]
  • CHP1:calcineurin like EF-hand protein 1 [Gene - OMIM - HGNC]
  • CHST14:carbohydrate sulfotransferase 14 [Gene - OMIM - HGNC]
  • C15orf62:chromosome 15 open reading frame 62 [Gene - HGNC]
  • CCDC32:coiled-coil domain containing 32 [Gene - OMIM - HGNC]
  • CCDC9B:coiled-coil domain containing 9B [Gene - HGNC]
  • DLL4:delta like canonical Notch ligand 4 [Gene - OMIM - HGNC]
  • DPH6:diphthamine biosynthesis 6 [Gene - OMIM - HGNC]
  • DISP2:dispatched RND transporter family member 2 [Gene - OMIM - HGNC]
  • EIF2AK4:eukaryotic translation initiation factor 2 alpha kinase 4 [Gene - OMIM - HGNC]
  • EXD1:exonuclease 3'-5' domain containing 1 [Gene - HGNC]
  • FAM98B:family with sequence similarity 98 member B [Gene - OMIM - HGNC]
  • FSIP1:fibrous sheath interacting protein 1 [Gene - OMIM - HGNC]
  • GJD2:gap junction protein delta 2 [Gene - OMIM - HGNC]
  • GOLGA8A:golgin A8 family member A [Gene - OMIM - HGNC]
  • GOLGA8B:golgin A8 family member B [Gene - OMIM - HGNC]
  • ITPKA:inositol-trisphosphate 3-kinase A [Gene - OMIM - HGNC]
  • IVD:isovaleryl-CoA dehydrogenase [Gene - OMIM - HGNC]
  • KNSTRN:kinetochore localized astrin (SPAG5) binding protein [Gene - OMIM - HGNC]
  • KNL1:kinetochore scaffold 1 [Gene - OMIM - HGNC]
  • LTK:leukocyte receptor tyrosine kinase [Gene - OMIM - HGNC]
  • LINC02694:long intergenic non-protein coding RNA 2694 [Gene - HGNC]
  • LINC02915:long intergenic non-protein coding RNA 2915 [Gene - HGNC]
  • LPCAT4:lysophosphatidylcholine acyltransferase 4 [Gene - OMIM - HGNC]
  • NUSAP1:nucleolar and spindle associated protein 1 [Gene - OMIM - HGNC]
  • PAK6:p21 (RAC1) activated kinase 6 [Gene - OMIM - HGNC]
  • PLCB2:phospholipase C beta 2 [Gene - OMIM - HGNC]
  • PHGR1:proline, histidine and glycine rich 1 [Gene - HGNC]
  • PPP1R14D:protein phosphatase 1 regulatory inhibitor subunit 14D [Gene - OMIM - HGNC]
  • RHOV:ras homolog family member V [Gene - OMIM - HGNC]
  • RMDN3:regulator of microtubule dynamics 3 [Gene - OMIM - HGNC]
  • SPINT1:serine peptidase inhibitor, Kunitz type 1 [Gene - OMIM - HGNC]
  • SRP14:signal recognition particle 14 [Gene - OMIM - HGNC]
  • SPRED1:sprouty related EVH1 domain containing 1 [Gene - OMIM - HGNC]
  • THBS1:thrombospondin 1 [Gene - OMIM - HGNC]
  • TMCO5A:transmembrane and coiled-coil domains 5A [Gene - HGNC]
  • ZFYVE19:zinc finger FYVE-type containing 19 [Gene - OMIM - HGNC]
  • ZNF770:zinc finger protein 770 [Gene - HGNC]
Variant type:
Complex
Cytogenetic location:
15q14-15.1
Genomic location:
Chr15: 34638237 - 42057083 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 15q14-15.1 chr15:34638237..42057083 complex variant

Condition(s)

Name:
Spindle cell sarcoma
Identifiers:
MONDO: MONDO:0002927; MedGen: C0205945

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000804554Papaemmanuil Lab, Memorial Sloan Kettering Cancer Research Center
criteria provided, single submitter

(OnkoKB guidelines, 2017)
Pathogenic
(Aug 27, 2018)
somaticresearch

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedsomaticyes1not providednot provided1not providedresearch

Citations

PubMed

OncoKB: A Precision Oncology Knowledge Base.

Chakravarty D, Gao J, Phillips SM, Kundra R, Zhang H, Wang J, Rudolph JE, Yaeger R, Soumerai T, Nissan MH, Chang MT, Chandarlapaty S, Traina TA, Paik PK, Ho AL, Hantash FM, Grupe A, Baxi SS, Callahan MK, Snyder A, Chi P, Danila D, et al.

JCO Precis Oncol. 2017 Jul;2017. doi: 10.1200/PO.17.00011. Epub 2017 May 16.

PubMed [citation]
PMID:
28890946
PMCID:
PMC5586540

Details of each submission

From Papaemmanuil Lab, Memorial Sloan Kettering Cancer Research Center, SCV000804554.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (1)

Description

Given prior descriptions of oncogenic effect of NUTM1 fusions in literature, we consider this variant to be pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1somaticyes1not providednot provided1not providednot providednot provided

Last Updated: Nov 5, 2022