NM_000284.4(PDHA1):c.795A>G (p.Ala265=) AND Pyruvate dehydrogenase E1-alpha deficiency

Clinical significance:Benign (Last evaluated: Nov 25, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001166390.2

Allele description [Variation Report for NM_000284.4(PDHA1):c.795A>G (p.Ala265=)]

NM_000284.4(PDHA1):c.795A>G (p.Ala265=)

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.795A>G (p.Ala265=)
Other names:
p.A265A:GCA>GCG
HGVS:
  • NC_000023.11:g.19355721A>G
  • NG_016781.1:g.16829A>G
  • NM_000284.4:c.795A>GMANE SELECT
  • NM_001173454.1:c.909A>G
  • NM_001173455.1:c.816A>G
  • NM_001173456.1:c.702A>G
  • NP_000275.1:p.Ala265=
  • NP_001166925.1:p.Ala303=
  • NP_001166926.1:p.Ala272=
  • NP_001166927.1:p.Ala234=
  • NC_000023.10:g.19373839A>G
  • NM_000284.2:c.795A>G
  • NM_000284.3:c.795A>G
  • NP_000275.1:p.(=)
  • NP_000275.1:p.(=)
  • NP_000275.1:p.(=)
Links:
dbSNP: rs1126565
NCBI 1000 Genomes Browser:
rs1126565
Molecular consequence:
  • NM_000284.4:c.795A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001173454.1:c.909A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001173455.1:c.816A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001173456.1:c.702A>G - synonymous variant - [Sequence Ontology: SO:0001819]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001328765Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Benign
(Apr 28, 2017)
germlineclinical testing

Citation Link,

SCV001720554Invitaecriteria provided, single submitter
Benign
(Nov 25, 2020)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV001328765.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.

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

From Invitae, SCV001720554.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 18, 2021

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