Is DLAT p.Val534= (c.1602G>A) pathogenic?

DLAT p.Val534= (c.1602G>A) is classified Likely benign in DLAT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-21). Very rare (popmax 0.00134%, afr); Associated with pyruvate dehydrogenase E2 deficiency.

What condition is associated with DLAT p.Val534= (c.1602G>A)?

DLAT p.Val534= (c.1602G>A) is associated with pyruvate dehydrogenase E2 deficiency (ClinVar).

How common is DLAT p.Val534= (c.1602G>A) in the general population?

DLAT p.Val534= (c.1602G>A) is very rare (popmax 0.00134%, afr) (gnomAD).

How is Pyruvate dehydrogenase deficiency inherited?

Typically Autosomal recessive, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

DLAT p.Val534=

c.1602G>A · VCV4715245

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Conditions

pyruvate dehydrogenase E2 deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.9	GERP 1.7, phastCons 1
Overall
CADD	11.5	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,856 alleles

Overall 0.000658% 1/152,012 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DLAT
Protein: p.Val534=
Coding: c.1602G>A
MANE Select: NM_138789 · reported on NM_001931
Type: single nucleotide variant
Location: chr11:112059990 (GRCh38)

Full DLAT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

pyruvate dehydrogenase E2 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Pyruvate dehydrogenase deficiency (Orphanet):

Inheritance: Autosomal recessive, Not applicable, X-linked dominant
Onset: Childhood, Infancy, Neonatal

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dlat-p-val534 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown