NM_003000.3(SDHB):c.141G>A (p.Trp47Ter) AND multiple conditions

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 14, 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:: RCV000474236.6

Allele description

NM_003000.3(SDHB):c.141G>A (p.Trp47Ter)

Gene:

SDHB:succinate dehydrogenase complex iron sulfur subunit B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.13

Genomic location:

Preferred name:

NM_003000.3(SDHB):c.141G>A (p.Trp47Ter)

HGVS:

NC_000001.11:g.17044820C>T
NG_012340.1:g.14351G>A
NM_003000.3:c.141G>AMANE SELECT
NP_002991.2:p.Trp47Ter
NP_002991.2:p.Trp47Ter
LRG_316t1:c.141G>A
LRG_316:g.14351G>A
LRG_316p1:p.Trp47Ter
NC_000001.10:g.17371315C>T
NM_003000.2:c.141G>A

Protein change:

W47*

Links:

dbSNP: rs1060503762

NCBI 1000 Genomes Browser:

rs1060503762

Molecular consequence:

NM_003000.3:c.141G>A - nonsense - [Sequence Ontology: SO:0001587]

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 4 (PPGL4)
Synonyms:: CAROTID BODY TUMORS AND MULTIPLE EXTRAADRENAL PHEOCHROMOCYTOMAS; Pheochromocytoma, extraadrenal and cervical paraganglioma; Paragangliomas, hereditary extraadrenal; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007273; MedGen: C1861848; Orphanet: 29072; OMIM: 115310

Name:: Pheochromocytoma
Synonyms:: Chromaffinoma; Chromaffin paraganglioma; Chromaffin tumor; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008233; MedGen: C0031511; Orphanet: 29072; OMIM: 171300; Human Phenotype Ontology: HP:0002666

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000554009	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 14, 2023)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 16405730, 18419787, 21348866, 29386252, 19454582, 19802898, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000554009

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 14, 2023)

germline

clinical testing

PubMed (7)
[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

Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

Bayley JP, van Minderhout I, Weiss MM, Jansen JC, Oomen PH, Menko FH, Pasini B, Ferrando B, Wong N, Alpert LC, Williams R, Blair E, Devilee P, Taschner PE.

BMC Med Genet. 2006 Jan 11;7:1.

PubMed [citation]

PMID:: 16405730
PMCID:: PMC1343542

Clinical manifestations of familial paraganglioma and phaeochromocytomas in succinate dehydrogenase B (SDH-B) gene mutation carriers.

Srirangalingam U, Walker L, Khoo B, MacDonald F, Gardner D, Wilkin TJ, Skelly RH, George E, Spooner D, Monson JP, Grossman AB, Akker SA, Pollard PJ, Plowman N, Avril N, Berney DM, Burrin JM, Reznek RH, Kumar VK, Maher ER, Chew SL.

Clin Endocrinol (Oxf). 2008 Oct;69(4):587-96. doi: 10.1111/j.1365-2265.2008.03274.x. Epub 2008 Apr 14.

PubMed [citation]

PMID:: 18419787

See all PubMed Citations (7)

Details of each submission

From Invitae, SCV000554009.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 412474). This premature translational stop signal has been observed in individual(s) with paraganglioma, pheochromocytoma, and renal cell carcinoma (PMID: 16405730, 18419787, 21348866, 29386252). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp47*) in the SDHB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SDHB are known to be pathogenic (PMID: 19454582, 19802898).

#	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: Sep 16, 2024

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