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NM_003001.5(SDHC):c.367C>T (p.Pro123Ser) AND Hereditary pheochromocytoma-paraganglioma

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 13, 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:
RCV004004764.2

Allele description [Variation Report for NM_003001.5(SDHC):c.367C>T (p.Pro123Ser)]

NM_003001.5(SDHC):c.367C>T (p.Pro123Ser)

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.367C>T (p.Pro123Ser)
HGVS:
  • NC_000001.11:g.161356802C>T
  • NG_012767.1:g.47427C>T
  • NM_001035511.3:c.242-5527C>T
  • NM_001035512.3:c.265C>T
  • NM_001035513.3:c.208C>T
  • NM_001278172.3:c.140-5527C>T
  • NM_001407115.1:c.487C>T
  • NM_001407116.1:c.310C>T
  • NM_001407117.1:c.304C>T
  • NM_001407118.1:c.259C>T
  • NM_001407119.1:c.256C>T
  • NM_001407120.1:c.256C>T
  • NM_001407121.1:c.185-5527C>T
  • NM_003001.5:c.367C>TMANE SELECT
  • NP_001030589.1:p.Pro89Ser
  • NP_001030590.1:p.Pro70Ser
  • NP_001394044.1:p.Pro163Ser
  • NP_001394045.1:p.Pro104Ser
  • NP_001394046.1:p.Pro102Ser
  • NP_001394047.1:p.Pro87Ser
  • NP_001394048.1:p.Pro86Ser
  • NP_001394049.1:p.Pro86Ser
  • NP_002992.1:p.Pro123Ser
  • NP_002992.1:p.Pro123Ser
  • LRG_317t1:c.367C>T
  • LRG_317:g.47427C>T
  • LRG_317p1:p.Pro123Ser
  • NC_000001.10:g.161326592C>T
  • NM_003001.3:c.367C>T
  • NR_103459.3:n.419C>T
Protein change:
P102S
Links:
dbSNP: rs773039986
NCBI 1000 Genomes Browser:
rs773039986
Molecular consequence:
  • NM_001035511.3:c.242-5527C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001278172.3:c.140-5527C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001407121.1:c.185-5527C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001035512.3:c.265C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001035513.3:c.208C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407115.1:c.487C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407116.1:c.310C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407117.1:c.304C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407118.1:c.259C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407119.1:c.256C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407120.1:c.256C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003001.5:c.367C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_103459.3:n.419C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
7

Condition(s)

Name:
Hereditary pheochromocytoma-paraganglioma
Synonyms:
Hereditary Paraganglioma-Pheochromocytoma Syndromes; Hereditary Paragangliomas and Pheochromocytomas
Identifiers:
MONDO: MONDO:0017366; MedGen: C1708353

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004822185All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain Significance
(Dec 13, 2023) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown7not providednot provided108544not providedclinical testing

Citations

PubMed

Vitamin E protects against lipid peroxidation and rescues tumorigenic phenotypes in cowden/cowden-like patient-derived lymphoblast cells with germline SDHx variants.

Ni Y, Eng C.

Clin Cancer Res. 2012 Sep 15;18(18):4954-61. Epub 2012 Jul 24.

PubMed [citation]
PMID:
22829200
PMCID:
PMC3445717

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From All of Us Research Program, National Institutes of Health, SCV004822185.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided7not providednot providedclinical testing PubMed (2)

Description

This missense variant replaces proline with serine at codon 123 of the SDHC protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with SDHC-related disorders in the literature, however the variant has been observed in patients with PTEN mutation negative Cowden/Cowden-like syndrome (PMID: 22829200). This variant has been identified in 7/280430 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided7not providednot providednot provided

Last Updated: Sep 29, 2024