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NM_003477.3(PDHX):c.531C>T (p.Pro177=) AND Pyruvate dehydrogenase E3-binding protein deficiency

Germline classification:
Benign (2 submissions)
Last evaluated:
Nov 22, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000276511.11

Allele description [Variation Report for NM_003477.3(PDHX):c.531C>T (p.Pro177=)]

NM_003477.3(PDHX):c.531C>T (p.Pro177=)

Gene:
PDHX:pyruvate dehydrogenase complex component X [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p13
Genomic location:
Preferred name:
NM_003477.3(PDHX):c.531C>T (p.Pro177=)
Other names:
p.P177P:CCC>CCT
HGVS:
  • NC_000011.10:g.34957572C>T
  • NG_013368.1:g.46443C>T
  • NM_001135024.2:c.351C>T
  • NM_001166158.2:c.342+9966C>T
  • NM_003477.3:c.531C>TMANE SELECT
  • NP_001128496.2:p.Pro117=
  • NP_003468.2:p.Pro177=
  • NC_000011.9:g.34979119C>T
  • NM_003477.2:c.531C>T
Links:
dbSNP: rs76486106
NCBI 1000 Genomes Browser:
rs76486106
Molecular consequence:
  • NM_001166158.2:c.342+9966C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001135024.2:c.351C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_003477.3:c.531C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Pyruvate dehydrogenase E3-binding protein deficiency (PDHXD)
Synonyms:
LACTIC ACIDEMIA DUE TO DEFECT IN LIPOYL-CONTAINING COMPONENT X OF THE PYRUVATE DEHYDROGENASE COMPLEX; Lacticacidemia due to PDX1 deficiency; PYRUVATE HYDROGENASE E3-BINDING PROTEIN DEFICIENCY; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009503; MedGen: C1855553; OMIM: 245349

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000371618Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Benign
(Jan 12, 2018) 		germlineclinical testing

Citation Link,

SCV002047933ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)		Benign
(Nov 22, 2023) 		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, SCV000371618.3

#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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002047933.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024