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NM_000284.4(PDHA1):c.1000G>A (p.Glu334Lys) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 11, 2019
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:
RCV001281432.2

Allele description [Variation Report for NM_000284.4(PDHA1):c.1000G>A (p.Glu334Lys)]

NM_000284.4(PDHA1):c.1000G>A (p.Glu334Lys)

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.1000G>A (p.Glu334Lys)
HGVS:
  • NC_000023.11:g.19359016G>A
  • NG_016781.1:g.20124G>A
  • NG_021184.1:g.161246C>T
  • NM_000284.4:c.1000G>AMANE SELECT
  • NM_001173454.2:c.1114G>A
  • NM_001173455.2:c.1021G>A
  • NM_001173456.2:c.907G>A
  • NP_000275.1:p.Glu334Lys
  • NP_001166925.1:p.Glu372Lys
  • NP_001166926.1:p.Glu341Lys
  • NP_001166927.1:p.Glu303Lys
  • NC_000023.10:g.19377134G>A
  • NM_000284.3:c.1000G>A
Protein change:
E303K
Links:
dbSNP: rs1269552788
NCBI 1000 Genomes Browser:
rs1269552788
Molecular consequence:
  • NM_000284.4:c.1000G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001173454.2:c.1114G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001173455.2:c.1021G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001173456.2:c.907G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Seizure
Synonyms:
Seizures
Identifiers:
MedGen: C0036572; Human Phenotype Ontology: HP:0001250
Name:
Intellectual disability
Synonyms:
Intellectual functioning disability; intellectual disabilities; Intellectual developmental disorder
Identifiers:
MONDO: MONDO:0001071; MeSH: D008607; MedGen: C3714756; Human Phenotype Ontology: HP:0001249

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001468740New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Jun 11, 2019) 		maternalclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedmaternalyes1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV001468740.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The maternally inherited hemizygous p.Glu334Lys variant identified in this individual has not been reported in the medical literature. The variant has 0.00001 allele frequency in the gnomAD database [2 out of 183,051 heterozygous alleles, no hemizygous allele] indicating it is an extremely rare allele in the populations represented in that database. The p.Glu334Lys affects a highly conserved residue and is predicted deleterious by a variety of in silico prediction tools. Based on the current evidence, the p.Glu334Lysvariant in the PDHA1 gene is assessed as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyes1not providednot provided1not providednot providednot provided

Last Updated: Sep 29, 2024