NM_003477.3(PDHX):c.70C>T (p.Arg24Ter) AND Pyruvate dehydrogenase E3-binding protein deficiency

Germline classification:: Likely pathogenic (1 submission)
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:: RCV003986041.1

Allele description [Variation Report for NM_003477.3(PDHX):c.70C>T (p.Arg24Ter)]

NM_003477.3(PDHX):c.70C>T (p.Arg24Ter)

Genes:

LOC130005549:ATAC-STARR-seq lymphoblastoid active region 4608 [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.70C>T (p.Arg24Ter)

HGVS:

NC_000011.10:g.34916725C>T
NG_013368.1:g.5596C>T
NG_184994.1:g.206C>T
NM_001135024.2:c.-21+239C>T
NM_001166158.2:c.70C>T
NM_003477.3:c.70C>TMANE SELECT
NP_001159630.1:p.Arg24Ter
NP_003468.2:p.Arg24Ter
NC_000011.9:g.34938272C>T

Protein change:

R24*

Molecular consequence:

NM_001135024.2:c.-21+239C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001166158.2:c.70C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_003477.3:c.70C>T - nonsense - [Sequence Ontology: SO:0001587]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004801881	Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004801881

Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, SCV004801881.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

A previously undescribed nucleotide variant creates a premature translation stop signal p.Arg24Ter in the PDHX gene. The variant was observed in homozygous state in an individual affected with motor delay and intellectual deficiency. Homozygous and compound heterozygous variants are reported in patients with Lacticacidemia due to PDX1 deficiency, 245349. The variant is not present in population database (gnomAD no frequency). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as likely pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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