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NM_003002.4(SDHD):c.317G>T (p.Gly106Val) AND SDHD-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 15, 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:
RCV003420005.4

Allele description [Variation Report for NM_003002.4(SDHD):c.317G>T (p.Gly106Val)]

NM_003002.4(SDHD):c.317G>T (p.Gly106Val)

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.317G>T (p.Gly106Val)
HGVS:
  • NC_000011.10:g.112094807G>T
  • NG_012337.3:g.12961G>T
  • NM_001276503.2:c.172G>T
  • NM_001276504.2:c.200G>T
  • NM_001276506.2:c.*15G>T
  • NM_003002.4:c.317G>TMANE SELECT
  • NP_001263432.1:p.Ala58Ser
  • NP_001263433.1:p.Gly67Val
  • NP_002993.1:p.Gly106Val
  • LRG_9t1:c.317G>T
  • LRG_9:g.12961G>T
  • LRG_9p1:p.Gly106Val
  • NC_000011.9:g.111965531G>T
  • NM_003002.2:c.317G>T
  • NM_003002.3:c.317G>T
  • NR_077060.2:n.406G>T
Protein change:
A58S
Links:
dbSNP: rs1555187574
NCBI 1000 Genomes Browser:
rs1555187574
Molecular consequence:
  • NM_001276506.2:c.*15G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001276503.2:c.172G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276504.2:c.200G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003002.4:c.317G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_077060.2:n.406G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
SDHD-related disorder
Synonyms:
SDHD-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004107262PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Sep 15, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004107262.1

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

Description

The SDHD c.317G>T variant is predicted to result in the amino acid substitution p.Gly106Val. This variant has been reported in multiple individuals with pheochromocytomas and/or paragangliomas (Table S1, Neumann et al. 2009. PubMed ID: 19351833; Table S2, Garrett et al. 2022. PubMed ID: 34906457; Internal Data, PreventionGenetics). It has also been reported to co-segregate with pheochromocytoma-paraganglioma syndrome in two independent multigenerational families (Table 1, Knie et al. 2016. PubMed ID: 26740102; Figure 1, Trache et al. 2022. PubMed ID: 35582561). This variant is not present in a large population database (https://gnomad.broadinstitute.org/), indicating that it is rare. It is interpreted as likely pathogenic and pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/480806/). In addition, a different amino acid substitution at this position (p.Gly106Asp) was previously reported in several individuals with paraganglioma and is interpreted as pathogenic in ClinVar (Ogawa et al. 2006. PubMed ID: 17041923; Yamashita et al. 2009. PubMed ID: 19550080; Panizza et al. 2013. PubMed ID: 23175444; https://www.ncbi.nlm.nih.gov/clinvar/variation/1401809/). The c.317G>T (p.Gly106Val) variant is interpreted as likely pathogenic.

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

Last Updated: Oct 26, 2024