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NM_003001.5(SDHC):c.78-1G>T AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 23, 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:
RCV000641911.9

Allele description [Variation Report for NM_003001.5(SDHC):c.78-1G>T]

NM_003001.5(SDHC):c.78-1G>T

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.78-1G>T
HGVS:
  • NC_000001.11:g.161328395G>T
  • NG_012767.1:g.19020G>T
  • NM_001035511.3:c.78-1G>T
  • NM_001035512.3:c.77+4725G>T
  • NM_001035513.3:c.21-12199G>T
  • NM_001278172.3:c.77+4725G>T
  • NM_001407115.1:c.78-1G>T
  • NM_001407116.1:c.21-1G>T
  • NM_001407117.1:c.21-1G>T
  • NM_001407118.1:c.77+4725G>T
  • NM_001407119.1:c.-34-1G>T
  • NM_001407120.1:c.-34-1G>T
  • NM_001407121.1:c.21-1G>T
  • NM_003001.5:c.78-1G>TMANE SELECT
  • LRG_317t1:c.78-1G>T
  • LRG_317:g.19020G>T
  • NC_000001.10:g.161298185G>T
  • NM_003001.3:c.78-1G>T
Links:
dbSNP: rs786202200
NCBI 1000 Genomes Browser:
rs786202200
Molecular consequence:
  • NM_001035512.3:c.77+4725G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001035513.3:c.21-12199G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001278172.3:c.77+4725G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001407118.1:c.77+4725G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001035511.3:c.78-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407115.1:c.78-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407116.1:c.21-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407117.1:c.21-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407119.1:c.-34-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407120.1:c.-34-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407121.1:c.21-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_003001.5:c.78-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV000763561Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(May 23, 2023) 		germlineclinical testing

PubMed (6)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Clinical and molecular genetics of patients with the Carney-Stratakis syndrome and germline mutations of the genes coding for the succinate dehydrogenase subunits SDHB, SDHC, and SDHD.

Pasini B, McWhinney SR, Bei T, Matyakhina L, Stergiopoulos S, Muchow M, Boikos SA, Ferrando B, Pacak K, Assie G, Baudin E, Chompret A, Ellison JW, Briere JJ, Rustin P, Gimenez-Roqueplo AP, Eng C, Carney JA, Stratakis CA.

Eur J Hum Genet. 2008 Jan;16(1):79-88. Epub 2007 Aug 1.

PubMed [citation]
PMID:
17667967
See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000763561.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This sequence change affects an acceptor splice site in intron 2 of the SDHC gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SDHC are known to be pathogenic (PMID: 17667967, 19454582, 23282968, 24758179). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SDHC-related conditions. ClinVar contains an entry for this variant (Variation ID: 534370). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site.

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

Last Updated: Jan 13, 2025