NM_001931.5(DLAT):c.381+1G>T AND Pyruvate dehydrogenase E2 deficiency

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 7, 2023
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:: RCV003603261.2

Allele description [Variation Report for NM_001931.5(DLAT):c.381+1G>T]

NM_001931.5(DLAT):c.381+1G>T

Gene:

DLAT:dihydrolipoamide S-acetyltransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.1

Genomic location:

Preferred name:

NM_001931.5(DLAT):c.381+1G>T

HGVS:

NC_000011.10:g.112026300G>T
NG_013342.1:g.6487G>T
NM_001372031.1:c.381+1G>T
NM_001372032.1:c.381+1G>T
NM_001372033.1:c.381+1G>T
NM_001372034.1:c.348+1G>T
NM_001372035.1:c.381+1G>T
NM_001372036.1:c.255+1G>T
NM_001372037.1:c.213+1G>T
NM_001372038.1:c.381+1G>T
NM_001372039.1:c.381+1G>T
NM_001372040.1:c.364+18G>T
NM_001372041.1:c.381+1G>T
NM_001372042.1:c.-86+1G>T
NM_001931.5:c.381+1G>TMANE SELECT
NC_000011.9:g.111897024G>T

Molecular consequence:

NM_001372040.1:c.364+18G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001372031.1:c.381+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001372032.1:c.381+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001372033.1:c.381+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001372034.1:c.348+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001372035.1:c.381+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001372036.1:c.255+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001372037.1:c.213+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001372038.1:c.381+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001372039.1:c.381+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001372041.1:c.381+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001372042.1:c.-86+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001931.5:c.381+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Pyruvate dehydrogenase E2 deficiency (PDHDD)
Synonyms:: LACTIC ACIDEMIA DUE TO DEFECT OF E2 LIPOYL TRANSACETYLASE OF THE PYRUVATE DEHYDROGENASE COMPLEX; Dihydrolipoamide Acetyltransferase (E2) Deficiency
Identifiers:: MONDO: MONDO:0009502; MedGen: C1855565; Orphanet: 765; Orphanet: 79244; OMIM: 245348

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004379137	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Sep 7, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16199547, 20022530, 23021068, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004379137

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Sep 7, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Pyruvate dehydrogenase E2 deficiency: a potentially treatable cause of episodic dystonia.

McWilliam CA, Ridout CK, Brown RM, McWilliam RC, Tolmie J, Brown GK.

Eur J Paediatr Neurol. 2010 Jul;14(4):349-53. doi: 10.1016/j.ejpn.2009.11.001. Epub 2009 Dec 21.

PubMed [citation]

PMID:: 20022530

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004379137.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This sequence change affects a donor splice site in intron 2 of the DLAT gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in DLAT are known to be pathogenic (PMID: 20022530, 23021068). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with DLAT-related conditions. 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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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