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NM_003001.5(SDHC):c.250_251del (p.Leu84fs) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 2, 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:
RCV001380966.5

Allele description [Variation Report for NM_003001.5(SDHC):c.250_251del (p.Leu84fs)]

NM_003001.5(SDHC):c.250_251del (p.Leu84fs)

Gene:
SDHC:succinate dehydrogenase complex subunit C [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
1q23.3
Genomic location:
Preferred name:
NM_003001.5(SDHC):c.250_251del (p.Leu84fs)
HGVS:
  • NC_000001.11:g.161356681CT[2]
  • NG_012767.1:g.47306CT[2]
  • NM_001035511.3:c.242-5649TC[2]
  • NM_001035512.3:c.148_149del
  • NM_001035513.3:c.91_92del
  • NM_001278172.3:c.140-5649TC[2]
  • NM_001407115.1:c.370_371del
  • NM_001407116.1:c.193_194del
  • NM_001407117.1:c.187_188del
  • NM_001407118.1:c.142_143del
  • NM_001407119.1:c.139_140del
  • NM_001407120.1:c.139_140del
  • NM_001407121.1:c.185-5649TC[2]
  • NM_003001.5:c.250_251delMANE SELECT
  • NP_001030589.1:p.Leu50fs
  • NP_001030590.1:p.Leu31fs
  • NP_001394044.1:p.Leu124fs
  • NP_001394045.1:p.Leu65fs
  • NP_001394046.1:p.Leu63fs
  • NP_001394047.1:p.Leu48fs
  • NP_001394048.1:p.Leu47fs
  • NP_001394049.1:p.Leu47fs
  • NP_002992.1:p.Leu84Phefs
  • NP_002992.1:p.Leu84fs
  • LRG_317t1:c.246_247CT[2]
  • LRG_317:g.47306CT[2]
  • LRG_317p1:p.Leu84Phefs
  • NC_000001.10:g.161326470_161326471del
  • NC_000001.10:g.161326471CT[2]
  • NM_003001.3:c.246_247CT[2]
  • NM_003001.3:c.250_251delCT
  • NR_103459.3:n.298CT[2]
Protein change:
L124fs
Links:
dbSNP: rs2102370242
NCBI 1000 Genomes Browser:
rs2102370242
Molecular consequence:
  • NM_001035512.3:c.148_149del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001035513.3:c.91_92del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407115.1:c.370_371del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407116.1:c.193_194del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407117.1:c.187_188del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407118.1:c.142_143del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407119.1:c.139_140del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407120.1:c.139_140del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_003001.5:c.250_251del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001035511.3:c.242-5649TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001278172.3:c.140-5649TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001407121.1:c.185-5649TC[2] - intron variant - [Sequence Ontology: SO:0001627]
  • NR_103459.3:n.298CT[2] - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001579200Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Mar 2, 2023) 		germlineclinical testing

PubMed (5)
[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

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

The succinate dehydrogenase genetic testing in a large prospective series of patients with paragangliomas.

Burnichon N, Rohmer V, Amar L, Herman P, Leboulleux S, Darrouzet V, Niccoli P, Gaillard D, Chabrier G, Chabolle F, Coupier I, Thieblot P, Lecomte P, Bertherat J, Wion-Barbot N, Murat A, Venisse A, Plouin PF, Jeunemaitre X, Gimenez-Roqueplo AP; PGL.NET network..

J Clin Endocrinol Metab. 2009 Aug;94(8):2817-27. doi: 10.1210/jc.2008-2504. Epub 2009 May 19.

PubMed [citation]
PMID:
19454582
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001579200.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. This sequence change creates a premature translational stop signal (p.Leu84Phefs*13) in the SDHC gene. It is expected to result in an absent or disrupted protein product. 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 premature translational stop signal has been observed in individual(s) with paraganglioma (Invitae).

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

Last Updated: May 12, 2024