NM_003002.4(SDHD):c.209G>C (p.Arg70Thr) AND Hereditary cancer-predisposing syndrome

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

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 1, 2019
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:: RCV001014432.2

Allele description

NM_003002.4(SDHD):c.209G>C (p.Arg70Thr)

Gene:

SDHD:succinate dehydrogenase complex subunit D [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.1

Genomic location:

Preferred name:

NM_003002.4(SDHD):c.209G>C (p.Arg70Thr)

HGVS:

NC_000011.10:g.112088906G>C
NG_012337.3:g.7060G>C
NG_033145.1:g.2893C>G
NM_001276503.2:c.169+933G>C
NM_001276504.2:c.92G>C
NM_001276506.2:c.209G>C
NM_003002.4:c.209G>CMANE SELECT
NP_001263433.1:p.Arg31Thr
NP_001263435.1:p.Arg70Thr
NP_002993.1:p.Arg70Thr
LRG_9t1:c.209G>C
LRG_9:g.7060G>C
LRG_9p1:p.Arg70Thr
NC_000011.9:g.111959630G>C
NC_000011.9:g.111959630G>C
NM_003002.2:c.209G>C
NR_077060.2:n.244G>C

Protein change:

R31T

Links:

dbSNP: rs755047928

NCBI 1000 Genomes Browser:

rs755047928

Molecular consequence:

NM_001276503.2:c.169+933G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001276504.2:c.92G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276506.2:c.209G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003002.4:c.209G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_077060.2:n.244G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001175136	Ambry Genetics	criteria provided, single submitter (Ambry General Variant Classification Scheme_2022)	Likely pathogenic (Jul 1, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19454582, 22517557, 30172768 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001175136

Ambry Genetics

criteria provided, single submitter

(Ambry General Variant Classification Scheme_2022)

Likely pathogenic
(Jul 1, 2019)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

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	1	not provided	clinical testing

Citations

PubMed

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

A decade (2001-2010) of genetic testing for pheochromocytoma and paraganglioma.

Buffet A, Venisse A, Nau V, Roncellin I, Boccio V, Le Pottier N, Boussion M, Travers C, Simian C, Burnichon N, Abermil N, Favier J, Jeunemaitre X, Gimenez-Roqueplo AP.

Horm Metab Res. 2012 May;44(5):359-66. doi: 10.1055/s-0032-1304594. Epub 2012 Apr 19. Review.

PubMed [citation]

PMID:: 22517557

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV001175136.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (3)

Description

The p.R70T variant (also known as c.209G>C), located in coding exon 3 of the SDHD gene, results from a G to C substitution at nucleotide position 209. The arginine at codon 70 is replaced by threonine, an amino acid with similar properties. This alteration has been identified in several patients with personal and family histories of paragangliomas (Burnichon N et al. J. Clin. Endocrinol. Metab. 2009 Aug;94:2817-27; Jiménez CM et al. Endocrinol Diabetes Nutr. 2018 Nov;65:508-514; Ambry internal data). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

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

Last Updated: Mar 5, 2024

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