NM_003001.5(SDHC):c.118C>G (p.Arg40Gly) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 24, 2023
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:: RCV000695000.11

Allele description [Variation Report for NM_003001.5(SDHC):c.118C>G (p.Arg40Gly)]

NM_003001.5(SDHC):c.118C>G (p.Arg40Gly)

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.118C>G (p.Arg40Gly)

HGVS:

NC_000001.11:g.161328436C>G
NG_012767.1:g.19061C>G
NM_001035511.3:c.118C>G
NM_001035512.3:c.77+4766C>G
NM_001035513.3:c.21-12158C>G
NM_001278172.3:c.77+4766C>G
NM_001407115.1:c.118C>G
NM_001407116.1:c.61C>G
NM_001407117.1:c.61C>G
NM_001407118.1:c.77+4766C>G
NM_001407119.1:c.7C>G
NM_001407120.1:c.7C>G
NM_001407121.1:c.61C>G
NM_003001.5:c.118C>GMANE SELECT
NP_001030588.1:p.Arg40Gly
NP_001394044.1:p.Arg40Gly
NP_001394045.1:p.Arg21Gly
NP_001394046.1:p.Arg21Gly
NP_001394048.1:p.Arg3Gly
NP_001394049.1:p.Arg3Gly
NP_001394050.1:p.Arg21Gly
NP_002992.1:p.Arg40Gly
NP_002992.1:p.Arg40Gly
LRG_317t1:c.118C>G
LRG_317:g.19061C>G
LRG_317p1:p.Arg40Gly
NC_000001.10:g.161298226C>G
NM_003001.3:c.118C>G
NR_103459.3:n.143C>G

Protein change:

R21G

Links:

dbSNP: rs978019587

NCBI 1000 Genomes Browser:

rs978019587

Molecular consequence:

NM_001035512.3:c.77+4766C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001035513.3:c.21-12158C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001278172.3:c.77+4766C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407118.1:c.77+4766C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001035511.3:c.118C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407115.1:c.118C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407116.1:c.61C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407117.1:c.61C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407119.1:c.7C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407120.1:c.7C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407121.1:c.61C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003001.5:c.118C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_103459.3:n.143C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Gastrointestinal stroma tumor
Synonyms:: Gastrointestinal stromal tumor; Gastrointestinal stromal tumor, somatic
Identifiers:: MONDO: MONDO:0011719; MeSH: D046152; MedGen: C0238198; Orphanet: 44890; OMIM: 606764; Human Phenotype Ontology: HP:0100723

Name:: Pheochromocytoma/paraganglioma syndrome 3
Synonyms:: GLOMUS TUMORS, FAMILIAL, 3; Paragangliomas 3; SDHC-Related Hereditary Paraganglioma-Pheochromocytoma Syndrome (Paragangliomas 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
SCV000823474	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 24, 2023)	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

SCV000823474

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 24, 2023)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000823474.5

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

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 40 of the SDHC protein (p.Arg40Gly). This variant has not been reported in the literature in individuals affected 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬¨‚Ä†is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 573349).

#	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: Jan 11, 2026

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