VCV000452714.5 - ClinVar

NM_001931.5(DLAT):c.367G>T (p.Asp123Tyr)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(3)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001931.5(DLAT):c.367G>T (p.Asp123Tyr)

Variation ID: 452714 Accession: VCV000452714.5

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 11q23.1 11: 112026285 (GRCh38) [ NCBI UCSC ] 11: 111897009 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Dec 19, 2017	Apr 15, 2024	Jan 31, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001931.5:c.367G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001922.2:p.Asp123Tyr	missense
NM_001372031.1:c.367G>T	NP_001358960.1:p.Asp123Tyr	missense
NM_001372032.1:c.367G>T	NP_001358961.1:p.Asp123Tyr	missense
NM_001372033.1:c.367G>T	NP_001358962.1:p.Asp123Tyr	missense
NM_001372034.1:c.334G>T	NP_001358963.1:p.Asp112Tyr	missense
NM_001372035.1:c.367G>T	NP_001358964.1:p.Asp123Tyr	missense
NM_001372036.1:c.241G>T	NP_001358965.1:p.Asp81Tyr	missense
NM_001372037.1:c.199G>T	NP_001358966.1:p.Asp67Tyr	missense
NM_001372038.1:c.367G>T	NP_001358967.1:p.Asp123Tyr	missense
NM_001372039.1:c.367G>T	NP_001358968.1:p.Asp123Tyr	missense
NM_001372040.1:c.364+3G>T		intron variant
NM_001372041.1:c.367G>T	NP_001358970.1:p.Asp123Tyr	missense
NM_001372042.1:c.-100G>T		5 prime UTR
NR_164072.1:n.432G>T		non-coding transcript variant
NC_000011.10:g.112026285G>T
NC_000011.9:g.111897009G>T
NG_013342.1:g.6472G>T

... more HGVS ... less HGVS

Protein change

D123Y, D112Y, D81Y, D67Y

Other names

p.D123Y

Canonical SPDI

NC_000011.10:112026284:G:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA382598087 dbSNP: rs1555179247 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
DLAT		-	-	GRCh38 GRCh37	262	343

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Uncertain significance (1)	criteria provided, single submitter	Jun 25, 2019	RCV000518970.2
Pyruvate dehydrogenase E2 deficiency	Uncertain significance (2)	criteria provided, single submitter	Jan 31, 2023	RCV003333076.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Jun 25, 2019)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV000621543.3 First in ClinVar: Dec 19, 2017 Last updated: Sep 24, 2021	Comment: Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has … (more) Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge (less)
Uncertain significance (Jan 31, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Pyruvate dehydrogenase E2 deficiency Affected status: unknown Allele origin: unknown	Baylor Genetics Accession: SCV004041338.1 First in ClinVar: Oct 07, 2023 Last updated: Oct 07, 2023
Uncertain significance (Dec 15, 2023)	no assertion criteria provided Method: clinical testing	Pyruvate dehydrogenase E2 deficiency (Autosomal recessive inheritance) Affected status: yes Allele origin: biparental	Undiagnosed Diseases Network, NIH Study: Undiagnosed Diseases Network (NIH), UDN Accession: SCV004812025.1 First in ClinVar: Apr 15, 2024 Last updated: Apr 15, 2024	Number of individuals with the variant: 3 Clinical Features: Microcephaly (present) , Strabismus (present) , Psychosis (present) , Global developmental delay (present) , Athetosis (present) , Short stature (present) , Cognitive impairment (present) Family history: yes Age: 20-29 years Sex: female Geographic origin: Iraq Tissue: Blood

Comment:

Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs1555179247 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Apr 15, 2024

ClinVar Genomic variation as it relates to human health

NM_001931.5(DLAT):c.367G>T (p.Asp123Tyr)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs1555179247 ...