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NM_000284.4(PDHA1):c.*319G>T AND Pyruvate dehydrogenase E1-alpha deficiency

Germline classification:
Benign (1 submission)
Last evaluated:
Jan 13, 2018
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:
RCV001166912.4

Allele description [Variation Report for NM_000284.4(PDHA1):c.*319G>T]

NM_000284.4(PDHA1):c.*319G>T

Gene:
PDHA1:pyruvate dehydrogenase E1 subunit alpha 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp22.12
Genomic location:
Preferred name:
NM_000284.4(PDHA1):c.*319G>T
HGVS:
  • NC_000023.11:g.19359972G>T
  • NG_016781.1:g.21080G>T
  • NG_021184.1:g.160290C>A
  • NM_000284.4:c.*319G>TMANE SELECT
  • NM_001173454.2:c.*319G>T
  • NM_001173455.2:c.*319G>T
  • NM_001173456.2:c.*319G>T
  • NC_000023.10:g.19378090G>T
  • NM_000284.3:c.*319G>T
Links:
dbSNP: rs1042449
NCBI 1000 Genomes Browser:
rs1042449
Molecular consequence:
  • NM_000284.4:c.*319G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001173454.2:c.*319G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001173455.2:c.*319G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001173456.2:c.*319G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]

Condition(s)

Name:
Pyruvate dehydrogenase E1-alpha deficiency (PDHAD)
Synonyms:
X-linked Leigh syndrome; ATAXIA, INTERMITTENT, WITH PYRUVATE DEHYDROGENASE DEFICIENCY; ATAXIA WITH LACTIC ACIDOSIS I; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010717; MedGen: C1839413; OMIM: 312170

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV001329338Illumina Laboratory Services, Illumina
    criteria provided, single submitter

    (ICSL Variant Classification Criteria 13 December 2019)    		Benign
    (Jan 13, 2018)     		germlineclinical testing

    Citation Link

    Help

    Summary from all submissions

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

    Details of each submission

    From Illumina Laboratory Services, Illumina, SCV001329338.1

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

    Description

    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.

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

    Last Updated: Sep 29, 2024