NM_003000.2(SDHB):c.308T>C (p.Met103Thr) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Aug 16, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000633951.1

Allele description [Variation Report for NM_003000.2(SDHB):c.308T>C (p.Met103Thr)]

NM_003000.2(SDHB):c.308T>C (p.Met103Thr)

Gene:
SDHB:succinate dehydrogenase complex iron sulfur subunit B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.13
Genomic location:
Preferred name:
NM_003000.2(SDHB):c.308T>C (p.Met103Thr)
HGVS:
  • NC_000001.11:g.17028715A>G
  • NG_012340.1:g.30456T>C
  • NM_003000.2:c.308T>C
  • NP_002991.2:p.Met103Thr
  • LRG_316t1:c.308T>C
  • LRG_316:g.30456T>C
  • LRG_316p1:p.Met103Thr
  • NC_000001.10:g.17355210A>G
Protein change:
M103T
Links:
dbSNP: rs1553177765
NCBI 1000 Genomes Browser:
rs1553177765
Molecular consequence:
  • NM_003000.2:c.308T>C - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000755224Invitaecriteria provided, single submitter
Uncertain significance
(Aug 16, 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

Magnetic resonance imaging spectrum of succinate dehydrogenase-related infantile leukoencephalopathy.

Helman G, Caldovic L, Whitehead MT, Simons C, Brockmann K, Edvardson S, Bai R, Moroni I, Taylor JM, Van Haren K; SDH Study Group., Taft RJ, Vanderver A, van der Knaap MS.

Ann Neurol. 2016 Mar;79(3):379-86. doi: 10.1002/ana.24572. Epub 2016 Feb 12. Erratum in: Ann Neurol. 2018 Sep;84(3):481.

PubMed [citation]
PMID:
26642834
PMCID:
PMC5712845

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, SCV000755224.1

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

Description

This sequence change replaces methionine with threonine at codon 103 of the SDHB protein (p.Met103Thr). The methionine residue is highly conserved and there is a moderate physicochemical difference between methionine and threonine. This variant is not present in population databases (ExAC no frequency). This variant has been reported in an individual affected with succinate dehydrogenase deficiency-related leukoencephalopathy (PMID: 26642834). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 7, 2021

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