NM_003000.2(SDHB):c.112del (p.Arg38fs) AND multiple conditions

Clinical significance:Pathogenic (Last evaluated: Nov 17, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000633966.1

Allele description [Variation Report for NM_003000.2(SDHB):c.112del (p.Arg38fs)]

NM_003000.2(SDHB):c.112del (p.Arg38fs)

Gene:
SDHB:succinate dehydrogenase complex iron sulfur subunit B [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p36.13
Genomic location:
Preferred name:
NM_003000.2(SDHB):c.112del (p.Arg38fs)
HGVS:
  • NC_000001.11:g.17044852del
  • NG_012340.1:g.14322del
  • NM_003000.2:c.112del
  • NP_002991.2:p.Arg38fs
  • LRG_316t1:c.112del
  • LRG_316:g.14322del
  • LRG_316p1:p.Arg38fs
  • NC_000001.10:g.17371347del
  • NM_003000.2:c.112delC
Protein change:
R38fs
Links:
dbSNP: rs398123690
NCBI 1000 Genomes Browser:
rs398123690
Molecular consequence:
  • NM_003000.2:c.112del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Gastrointestinal stromal tumor (GIST)
Synonyms:
Gastrointestinal Stromal Sarcoma; Gastrointestinal stromal tumor, somatic; Gastrointestinal stroma tumor; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011719; MeSH: D046152; MedGen: C0238198; Orphanet: 44890; OMIM: 606764; Human Phenotype Ontology: HP:0100723
Name:
Paragangliomas 4 (PGL4)
Synonyms:
CAROTID BODY TUMORS AND MULTIPLE EXTRAADRENAL PHEOCHROMOCYTOMAS; Pheochromocytoma, extraadrenal and cervical paraganglioma; Paragangliomas, hereditary extraadrenal; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007273; MedGen: C1861848; Orphanet: 29072; OMIM: 115310
Name:
Pheochromocytoma
Synonyms:
Chromaffinoma; Chromaffin paraganglioma; Chromaffin tumor; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008233; MedGen: C0031511; Orphanet: 29072; OMIM: 171300; Human Phenotype Ontology: HP:0002666

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000755239Invitaecriteria provided, single submitter
Pathogenic
(Nov 17, 2017)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Genetics of Apparently Sporadic Pheochromocytoma and Paraganglioma in a Chinese Population.

Lee CH, Cheung CY, Chow WS, Woo YC, Yeung CY, Lang BH, Fong CH, Kwok KH, Chen SP, Mak CM, Tan KC, Lam KS.

Horm Metab Res. 2015 Oct;47(11):833-8. doi: 10.1055/s-0035-1555955. Epub 2015 Aug 12.

PubMed [citation]
PMID:
26267327

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000755239.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Arg38Valfs*39) in the SDHB gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been reported in individuals affected with paraganglioma (PMID: 26267327, Invitae). Loss-of-function variants in SDHB are known to be pathogenic (PMID: 19454582, 19802898). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 7, 2021

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