NC_000001.10:g.(?_161284158)_(161284225_?)del AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 27, 2022
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:: RCV003113182.4

Allele description [Variation Report for NC_000001.10:g.(?_161284158)_(161284225_?)del]

NC_000001.10:g.(?_161284158)_(161284225_?)del

Gene:: SDHC:succinate dehydrogenase complex subunit C [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 1q23.3
Genomic location:: Chr1: 161284158 - 161284225 (on Assembly GRCh37)
Preferred name:: NC_000001.10:g.(?_161284158)_(161284225_?)del
HGVS:: NC_000001.10:g.(?_161284158)_(161284225_?)del
This HGVS expression did not pass validation

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
SCV003791264	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 27, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 17667967, 23282968, 24758179, 19454582, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003791264

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 27, 2022)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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

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

Immunohistochemical loss of succinate dehydrogenase subunit A (SDHA) in gastrointestinal stromal tumors (GISTs) signals SDHA germline mutation.

Miettinen M, Killian JK, Wang ZF, Lasota J, Lau C, Jones L, Walker R, Pineda M, Zhu YJ, Kim SY, Helman L, Meltzer P.

Am J Surg Pathol. 2013 Feb;37(2):234-40. doi: 10.1097/PAS.0b013e3182671178.

PubMed [citation]

PMID:: 23282968
PMCID:: PMC3545041

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV003791264.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 1 of the SDHC gene, which includes the initiator codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. 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). A similar copy number variant has been observed in individual(s) with head and neck and/or thoracic-abdominal pelvic paragangliomas (PMID: 19454582). For these reasons, this variant has been classified as Pathogenic.

#	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: May 12, 2024

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