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

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 5, 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:
RCV002232089.11

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:
Carney-Stratakis syndrome
Synonyms:
Paraganglioma and gastric stromal sarcoma; Paraganglioma and gastrointestinal stromal tumor; Paraganglioma and GIST; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011740; MedGen: C1847319; Orphanet: 97286; OMIM: 606864
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
Name:
Paragangliomas with sensorineural hearing loss (PGL1)
Identifiers:
MedGen: C1868633
Name:
Cowden syndrome 3 (CWS3)
Identifiers:
MONDO: MONDO:0014045; MedGen: CN166604; Orphanet: 201

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000961779Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 5, 2022) 		germlineclinical testing

PubMed (9)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Clinical predictors for germline mutations in head and neck paraganglioma patients: cost reduction strategy in genetic diagnostic process as fall-out.

Neumann HP, Erlic Z, Boedeker CC, Rybicki LA, Robledo M, Hermsen M, Schiavi F, Falcioni M, Kwok P, Bauters C, Lampe K, Fischer M, Edelman E, Benn DE, Robinson BG, Wiegand S, Rasp G, Stuck BA, Hoffmann MM, Sullivan M, Sevilla MA, Weiss MM, et al.

Cancer Res. 2009 Apr 15;69(8):3650-6. doi: 10.1158/0008-5472.CAN-08-4057. Epub 2009 Apr 7.

PubMed [citation]
PMID:
19351833

A novel G106D alteration of the SDHD gene in a pedigree with familial paraganglioma.

Ogawa K, Shiga K, Saijo S, Ogawa T, Kimura N, Horii A.

Am J Med Genet A. 2006 Nov 15;140(22):2441-6.

PubMed [citation]
PMID:
17041923
See all PubMed Citations (9)

Details of each submission

From Invitae, SCV000961779.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)

Description

ClinVar contains an entry for this variant (Variation ID: 480806). This missense change has been observed in individuals with hereditary paraganglioma-pheochromocytoma (PGL-PCC) syndrome (PMID: 19351833; Invitae; external communication). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 106 of the SDHD protein (p.Gly106Val). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Gly106 amino acid residue in SDHD. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17041923, 17102085, 19550080, 22241717, 22566194, 23175444, 29925701). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0").

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

Last Updated: May 1, 2024