NM_003001.5(SDHC):c.359T>G (p.Leu120Arg) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 19, 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:: RCV001321576.6

Allele description [Variation Report for NM_003001.5(SDHC):c.359T>G (p.Leu120Arg)]

NM_003001.5(SDHC):c.359T>G (p.Leu120Arg)

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.359T>G (p.Leu120Arg)

HGVS:

NC_000001.11:g.161356794T>G
NG_012767.1:g.47419T>G
NM_001035511.3:c.242-5535T>G
NM_001035512.3:c.257T>G
NM_001035513.3:c.200T>G
NM_001278172.3:c.140-5535T>G
NM_001407115.1:c.479T>G
NM_001407116.1:c.302T>G
NM_001407117.1:c.296T>G
NM_001407118.1:c.251T>G
NM_001407119.1:c.248T>G
NM_001407120.1:c.248T>G
NM_001407121.1:c.185-5535T>G
NM_003001.5:c.359T>GMANE SELECT
NP_001030589.1:p.Leu86Arg
NP_001030590.1:p.Leu67Arg
NP_001394044.1:p.Leu160Arg
NP_001394045.1:p.Leu101Arg
NP_001394046.1:p.Leu99Arg
NP_001394047.1:p.Leu84Arg
NP_001394048.1:p.Leu83Arg
NP_001394049.1:p.Leu83Arg
NP_002992.1:p.Leu120Arg
NP_002992.1:p.Leu120Arg
LRG_317t1:c.359T>G
LRG_317:g.47419T>G
LRG_317p1:p.Leu120Arg
NC_000001.10:g.161326584T>G
NM_003001.3:c.359T>G
NR_103459.3:n.411T>G

Protein change:

L101R

Links:

dbSNP: rs1672292051

NCBI 1000 Genomes Browser:

rs1672292051

Molecular consequence:

NM_001035511.3:c.242-5535T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001278172.3:c.140-5535T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407121.1:c.185-5535T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001035512.3:c.257T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001035513.3:c.200T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407115.1:c.479T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407116.1:c.302T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407117.1:c.296T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407118.1:c.251T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407119.1:c.248T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407120.1:c.248T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003001.5:c.359T>G - missense variant - [Sequence Ontology: SO:0001583]
NR_103459.3:n.411T>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001512412	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 19, 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

SCV001512412

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 19, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001512412.3

#	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: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1021759). This variant has not been reported in the literature in individuals affected with SDHC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 120 of the SDHC protein (p.Leu120Arg).

#	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 29, 2024

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