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NM_003001.5(SDHC):c.1A>G (p.Met1Val) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 26, 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:
RCV000791400.8

Allele description [Variation Report for NM_003001.5(SDHC):c.1A>G (p.Met1Val)]

NM_003001.5(SDHC):c.1A>G (p.Met1Val)

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.1A>G (p.Met1Val)
HGVS:
  • NC_000001.11:g.161314406A>G
  • NG_008055.1:g.567T>C
  • NG_012767.1:g.5031A>G
  • NM_001035511.3:c.1A>G
  • NM_001035512.3:c.1A>G
  • NM_001035513.3:c.1A>G
  • NM_001278172.3:c.1A>G
  • NM_001407115.1:c.1A>G
  • NM_001407116.1:c.1A>G
  • NM_001407117.1:c.1A>G
  • NM_001407118.1:c.1A>G
  • NM_001407119.1:c.-560A>G
  • NM_001407120.1:c.-229A>G
  • NM_001407121.1:c.1A>G
  • NM_003001.5:c.1A>GMANE SELECT
  • NP_001030588.1:p.Met1Val
  • NP_001030588.1:p.Met1Val
  • NP_001030589.1:p.Met1Val
  • NP_001030589.1:p.Met1Val
  • NP_001030590.1:p.Met1Val
  • NP_001030590.1:p.Met1Val
  • NP_001265101.1:p.Met1Val
  • NP_001265101.1:p.Met1Val
  • NP_001394044.1:p.Met1Val
  • NP_001394045.1:p.Met1Val
  • NP_001394046.1:p.Met1Val
  • NP_001394047.1:p.Met1Val
  • NP_001394050.1:p.Met1Val
  • NP_002992.1:p.Met1Val
  • NP_002992.1:p.Met1Val
  • LRG_317t1:c.1A>G
  • LRG_256:g.567T>C
  • LRG_317:g.5031A>G
  • LRG_317p1:p.Met1Val
  • NC_000001.10:g.161284196A>G
  • NM_001035511.2:c.1A>G
  • NM_001035512.2:c.1A>G
  • NM_001035513.2:c.1A>G
  • NM_001278172.2:c.1A>G
  • NM_003001.3:c.1A>G
  • NR_103459.2:n.26A>G
  • NR_103459.3:n.26A>G
Protein change:
M1V
Links:
dbSNP: rs755235380
NCBI 1000 Genomes Browser:
rs755235380
Molecular consequence:
  • NM_003001.5:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001035511.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001035512.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001035513.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001278172.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407115.1:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407116.1:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407117.1:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407118.1:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407121.1:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003001.5:c.1A>G - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000546039Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 26, 2023) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Mutations in SDHC cause autosomal dominant paraganglioma, type 3.

Niemann S, Müller U.

Nat Genet. 2000 Nov;26(3):268-70.

PubMed [citation]
PMID:
11062460

Predictors and prevalence of paraganglioma syndrome associated with mutations of the SDHC gene.

Schiavi F, Boedeker CC, Bausch B, Peçzkowska M, Gomez CF, Strassburg T, Pawlu C, Buchta M, Salzmann M, Hoffmann MM, Berlis A, Brink I, Cybulla M, Muresan M, Walter MA, Forrer F, Välimäki M, Kawecki A, Szutkowski Z, Schipper J, Walz MK, Pigny P, et al.

JAMA. 2005 Oct 26;294(16):2057-63. Erratum in: JAMA. 2006 Feb 8;295(6):628.

PubMed [citation]
PMID:
16249420
See all PubMed Citations (7)

Details of each submission

From Invitae, SCV000546039.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This sequence change affects the initiator methionine of the SDHC mRNA. The next in-frame methionine is located at codon 38. This variant is present in population databases (rs755235380, gnomAD 0.006%). Disruption of the initiator codon has been observed in individuals with clinical features of SDHC-related conditions (PMID: 11062460, 16249420, 19454582, 22351710, 22517554, 23282968). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 407060). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: May 1, 2024