NM_001931.5(DLAT):c.946C>T (p.Pro316Ser) AND Pyruvate dehydrogenase E2 deficiency

Germline classification:: Likely benign (3 submissions)
Last evaluated:: May 12, 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:: RCV000609986.5

Allele description [Variation Report for NM_001931.5(DLAT):c.946C>T (p.Pro316Ser)]

NM_001931.5(DLAT):c.946C>T (p.Pro316Ser)

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.946C>T (p.Pro316Ser)

HGVS:

NC_000011.10:g.112037431C>T
NG_013342.1:g.17618C>T
NM_001372031.1:c.946C>T
NM_001372032.1:c.946C>T
NM_001372033.1:c.946C>T
NM_001372034.1:c.913C>T
NM_001372035.1:c.946C>T
NM_001372036.1:c.820C>T
NM_001372037.1:c.778C>T
NM_001372038.1:c.667C>T
NM_001372039.1:c.661-1813C>T
NM_001372040.1:c.565C>T
NM_001372041.1:c.661-1813C>T
NM_001372042.1:c.484C>T
NM_001931.5:c.946C>TMANE SELECT
NP_001358960.1:p.Pro316Ser
NP_001358961.1:p.Pro316Ser
NP_001358962.1:p.Pro316Ser
NP_001358963.1:p.Pro305Ser
NP_001358964.1:p.Pro316Ser
NP_001358965.1:p.Pro274Ser
NP_001358966.1:p.Pro260Ser
NP_001358967.1:p.Pro223Ser
NP_001358969.1:p.Pro189Ser
NP_001358971.1:p.Pro162Ser
NP_001922.2:p.Pro316Ser
NP_001922.2:p.Pro316Ser
NC_000011.9:g.111908155C>T
NM_001931.4:c.946C>T

Protein change:

P162S

Links:

dbSNP: rs149088081

NCBI 1000 Genomes Browser:

rs149088081

Molecular consequence:

NM_001372039.1:c.661-1813C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001372041.1:c.661-1813C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001372031.1:c.946C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001372032.1:c.946C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001372033.1:c.946C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001372034.1:c.913C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001372035.1:c.946C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001372036.1:c.820C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001372037.1:c.778C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001372038.1:c.667C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001372040.1:c.565C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001372042.1:c.484C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001931.5:c.946C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000732998	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV000745137	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Aug 3, 2017)	germline	clinical testing	Citation Link,
SCV003269170	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (May 12, 2023)	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

SCV000732998

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus

no assertion criteria provided

Likely benign

germline

clinical testing

SCV000745137

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

criteria provided, single submitter

(ACGS Guidelines, 2013)

Likely benign
(Aug 3, 2017)

germline

clinical testing

Citation Link,

SCV003269170

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(May 12, 2023)

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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000732998.1

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

#	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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000745137.1

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

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003269170.2

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

#	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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