NM_001931.5(DLAT):c.55G>C (p.Glu19Gln) AND Pyruvate dehydrogenase E2 deficiency

Germline classification:: Benign (3 submissions)
Last evaluated:: Jan 29, 2024
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:: RCV001001506.19

Allele description [Variation Report for NM_001931.5(DLAT):c.55G>C (p.Glu19Gln)]

NM_001931.5(DLAT):c.55G>C (p.Glu19Gln)

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.55G>C (p.Glu19Gln)

Other names:

p.E19Q:GAG>CAG

HGVS:

NC_000011.10:g.112025527G>C
NG_013342.1:g.5714G>C
NM_001372031.1:c.55G>C
NM_001372032.1:c.55G>C
NM_001372033.1:c.55G>C
NM_001372034.1:c.55G>C
NM_001372035.1:c.55G>C
NM_001372036.1:c.14G>C
NM_001372037.1:c.14G>C
NM_001372038.1:c.55G>C
NM_001372039.1:c.55G>C
NM_001372040.1:c.55G>C
NM_001372041.1:c.55G>C
NM_001372042.1:c.-412G>C
NM_001931.5:c.55G>CMANE SELECT
NP_001358960.1:p.Glu19Gln
NP_001358961.1:p.Glu19Gln
NP_001358962.1:p.Glu19Gln
NP_001358963.1:p.Glu19Gln
NP_001358964.1:p.Glu19Gln
NP_001358965.1:p.Arg5Pro
NP_001358966.1:p.Arg5Pro
NP_001358967.1:p.Glu19Gln
NP_001358968.1:p.Glu19Gln
NP_001358969.1:p.Glu19Gln
NP_001358970.1:p.Glu19Gln
NP_001922.2:p.Glu19Gln
NP_001922.2:p.Glu19Gln
NC_000011.9:g.111896251G>C
NM_001931.4:c.55G>C
NR_164072.1:n.120G>C

Protein change:

E19Q

Links:

dbSNP: rs61757217

NCBI 1000 Genomes Browser:

rs61757217

Molecular consequence:

NM_001372042.1:c.-412G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001372031.1:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001372032.1:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001372033.1:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001372034.1:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001372035.1:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001372036.1:c.14G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001372037.1:c.14G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001372038.1:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001372039.1:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001372040.1:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001372041.1:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001931.5:c.55G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_164072.1:n.120G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000763846	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 29, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001158809	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Oct 14, 2023)	germline	clinical testing	Citation Link,
SCV001876763	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 30, 2021)	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

SCV000763846

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 29, 2024)

germline

clinical testing

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

SCV001158809

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Benign
(Oct 14, 2023)

germline

clinical testing

Citation Link,

SCV001876763

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jul 30, 2021)

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	no	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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000763846.7

#	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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001158809.2

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV001876763.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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