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NM_003001.5(SDHC):c.394A>G (p.Ile132Val) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 14, 2021
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:
RCV001944308.7

Allele description

NM_003001.5(SDHC):c.394A>G (p.Ile132Val)

Gene:
SDHC:succinate dehydrogenase complex subunit C [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q23.3
Genomic location:
Preferred name:
NM_003001.5(SDHC):c.394A>G (p.Ile132Val)
HGVS:
  • NC_000001.11:g.161356829A>G
  • NG_012767.1:g.47454A>G
  • NM_001035511.3:c.242-5500A>G
  • NM_001035512.3:c.292A>G
  • NM_001035513.3:c.235A>G
  • NM_001278172.3:c.140-5500A>G
  • NM_001407115.1:c.514A>G
  • NM_001407116.1:c.337A>G
  • NM_001407117.1:c.331A>G
  • NM_001407118.1:c.286A>G
  • NM_001407119.1:c.283A>G
  • NM_001407120.1:c.283A>G
  • NM_001407121.1:c.185-5500A>G
  • NM_003001.5:c.394A>GMANE SELECT
  • NP_001030589.1:p.Ile98Val
  • NP_001030590.1:p.Ile79Val
  • NP_001394044.1:p.Ile172Val
  • NP_001394045.1:p.Ile113Val
  • NP_001394046.1:p.Ile111Val
  • NP_001394047.1:p.Ile96Val
  • NP_001394048.1:p.Ile95Val
  • NP_001394049.1:p.Ile95Val
  • NP_002992.1:p.Ile132Val
  • NP_002992.1:p.Ile132Val
  • LRG_317t1:c.394A>G
  • LRG_317:g.47454A>G
  • LRG_317p1:p.Ile132Val
  • NC_000001.10:g.161326619A>G
  • NM_003001.3:c.394A>G
  • NR_103459.3:n.446A>G
Protein change:
I111V
Links:
dbSNP: rs2102371416
NCBI 1000 Genomes Browser:
rs2102371416
Molecular consequence:
  • NM_001035511.3:c.242-5500A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001278172.3:c.140-5500A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001407121.1:c.185-5500A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001035512.3:c.292A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001035513.3:c.235A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407115.1:c.514A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407116.1:c.337A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407117.1:c.331A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407118.1:c.286A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407119.1:c.283A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407120.1:c.283A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003001.5:c.394A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_103459.3:n.446A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Gastrointestinal stromal tumor
Synonyms:
Gastrointestinal Stromal Sarcoma; Gastrointestinal stromal tumor, somatic; Gastrointestinal stroma tumor
Identifiers:
MONDO: MONDO:0011719; MeSH: D046152; MedGen: C0238198; Orphanet: 44890; OMIM: 606764; Human Phenotype Ontology: HP:0100723
Name:
Paragangliomas 3 (PPGL3)
Synonyms:
Glomus tumors, familial, 3; SDHC-Related Hereditary Paraganglioma-Pheochromocytoma Syndrome (Paragangliomas 3); PHEOCHROMOCYTOMA/PARAGANGLIOMA SYNDROME 3
Identifiers:
MONDO: MONDO:0011544; MedGen: C1854336; Orphanet: 29072; OMIM: 605373

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002214704Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 14, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV002214704.3

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

Description

This variant has not been reported in the literature in individuals with SDHC-related conditions. 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SDHC protein function. This variant is not present in population databases (ExAC no frequency). This sequence change replaces isoleucine with valine at codon 132 of the SDHC protein (p.Ile132Val). The isoleucine residue is moderately conserved and there is a small physicochemical difference between isoleucine and valine.

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

Last Updated: Sep 16, 2024