NM_003001.5(SDHC):c.187C>T (p.Leu63Phe) AND multiple conditions

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 15, 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:: RCV001952335.7

Allele description

NM_003001.5(SDHC):c.187C>T (p.Leu63Phe)

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.187C>T (p.Leu63Phe)

HGVS:

NC_000001.11:g.161340601C>T
NG_012767.1:g.31226C>T
NM_001035511.3:c.187C>T
NM_001035512.3:c.85C>T
NM_001035513.3:c.28C>T
NM_001278172.3:c.85C>T
NM_001407115.1:c.307C>T
NM_001407116.1:c.130C>T
NM_001407117.1:c.130C>T
NM_001407118.1:c.85C>T
NM_001407119.1:c.76C>T
NM_001407120.1:c.76C>T
NM_001407121.1:c.130C>T
NM_003001.5:c.187C>TMANE SELECT
NP_001030588.1:p.Leu63Phe
NP_001030588.1:p.Leu63Phe
NP_001030589.1:p.Leu29Phe
NP_001030589.1:p.Leu29Phe
NP_001030590.1:p.Leu10Phe
NP_001030590.1:p.Leu10Phe
NP_001265101.1:p.Leu29Phe
NP_001265101.1:p.Leu29Phe
NP_001394044.1:p.Leu103Phe
NP_001394045.1:p.Leu44Phe
NP_001394046.1:p.Leu44Phe
NP_001394047.1:p.Leu29Phe
NP_001394048.1:p.Leu26Phe
NP_001394049.1:p.Leu26Phe
NP_001394050.1:p.Leu44Phe
NP_002992.1:p.Leu63Phe
NP_002992.1:p.Leu63Phe
LRG_317t1:c.187C>T
LRG_317:g.31226C>T
LRG_317p1:p.Leu63Phe
NC_000001.10:g.161310391C>T
NM_001035511.2:c.187C>T
NM_001035512.2:c.85C>T
NM_001035513.2:c.28C>T
NM_001278172.2:c.85C>T
NM_003001.3:c.187C>T
NR_103459.2:n.239C>T
NR_103459.3:n.239C>T

Protein change:

L103F

Links:

dbSNP: rs2102336071

NCBI 1000 Genomes Browser:

rs2102336071

Molecular consequence:

NM_001035511.3:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001035512.3:c.85C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001035513.3:c.28C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001278172.3:c.85C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407115.1:c.307C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407116.1:c.130C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407117.1:c.130C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407118.1:c.85C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407119.1:c.76C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407120.1:c.76C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407121.1:c.130C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003001.5:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002194996	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 15, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002194996

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 15, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV002194996.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with SDHC-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with phenylalanine at codon 63 of the SDHC protein (p.Leu63Phe). The leucine residue is moderately conserved and there is a small physicochemical difference between leucine and phenylalanine.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 16, 2024

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