NM_003000.3(SDHB):c.713del (p.Phe238fs) AND Hereditary pheochromocytoma-paraganglioma

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 8, 2024
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:: RCV003998576.2

Allele description [Variation Report for NM_003000.3(SDHB):c.713del (p.Phe238fs)]

NM_003000.3(SDHB):c.713del (p.Phe238fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

1p36.13

Genomic location:

Preferred name:

NM_003000.3(SDHB):c.713del (p.Phe238fs)

HGVS:

NC_000001.11:g.17022661del
NG_012340.1:g.36511del
NM_003000.3:c.713delMANE SELECT
NP_002991.2:p.Phe238fs
NP_002991.2:p.Phe238fs
LRG_316t1:c.713del
LRG_316:g.36511del
LRG_316p1:p.Phe238fs
NC_000001.10:g.17349155del
NC_000001.10:g.17349156del
NM_003000.2:c.713del
NM_003000.2:c.713delT

Protein change:

F238fs

Links:

dbSNP: rs876660642

NCBI 1000 Genomes Browser:

rs876660642

Molecular consequence:

NM_003000.3:c.713del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004822844	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 8, 2024)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 16317055, 19454582, 22517554, 28490599, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004822844

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 8, 2024)

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	1	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

Clinical presentation and penetrance of pheochromocytoma/paraganglioma syndromes.

Benn DE, Gimenez-Roqueplo AP, Reilly JR, Bertherat J, Burgess J, Byth K, Croxson M, Dahia PL, Elston M, Gimm O, Henley D, Herman P, Murday V, Niccoli-Sire P, Pasieka JL, Rohmer V, Tucker K, Jeunemaitre X, Marsh DJ, Plouin PF, Robinson BG.

J Clin Endocrinol Metab. 2006 Mar;91(3):827-36. Epub 2005 Nov 29.

PubMed [citation]

PMID:: 16317055

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 All of Us Research Program, National Institutes of Health, SCV004822844.1

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

Description

This variant deletes 1 nucleotide in exon 7 of the SDHB gene, creating a frameshift and premature translation stop signal in exon 7. This variant is predicted to escape nonsense-mediated decay and be expressed as a truncated protein. This variant has been reported in individuals affected with hereditary paraganglioma-pheochromocytoma syndrome (PMID: 16317055, 19454582, 22517554, 28490599). Downstream truncations are known to be disease-causing (ClinVar variation ID: 12782, 412481, 201607, 421424). This variant has been identified in 1/251466 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of SDHB function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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