NM_000108.5(DLD):c.249T>C (p.Val83=) AND Pyruvate dehydrogenase complex deficiency

Clinical significance:Benign (Last evaluated: Jan 13, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000108.5(DLD):c.249T>C (p.Val83=)]

NM_000108.5(DLD):c.249T>C (p.Val83=)

DLD:dihydrolipoamide dehydrogenase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000108.5(DLD):c.249T>C (p.Val83=)
Other names:
  • NC_000007.14:g.107902375T>C
  • NG_008045.1:g.16235T>C
  • NM_000108.5:c.249T>CMANE SELECT
  • NM_001289750.1:c.-30-1103T>C
  • NM_001289751.1:c.198+558T>C
  • NM_001289752.1:c.249T>C
  • NP_000099.2:p.Val83=
  • NP_001276681.1:p.Val83=
  • NC_000007.13:g.107542820T>C
  • NM_000108.3:c.249T>C
  • NM_000108.4:c.249T>C
  • p.Val83Val
dbSNP: rs2228664
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001289750.1:c.-30-1103T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001289751.1:c.198+558T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000108.5:c.249T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001289752.1:c.249T>C - synonymous variant - [Sequence Ontology: SO:0001819]


Pyruvate dehydrogenase complex deficiency (PDHC)
PDH DEFICIENCY; Pyruvate Dehydrogenase Complex Deficiency Disease; Pyruvate decarboxylase deficiency; See all synonyms [MedGen]
MONDO: MONDO:0019169; MedGen: C0034345; Orphanet: 765; Orphanet: 79243; OMIM: PS312170

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000466214Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
(Jan 13, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000466214.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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

Last Updated: Nov 10, 2021

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