Is ETFA p.Val263Gly (c.788T>G) pathogenic?

ETFA p.Val263Gly (c.788T>G) is classified Uncertain significance in ETFA (ClinVar, No assertion criteria, 1 submitter; last evaluated 2025-01-31). AlphaMissense: likely pathogenic (0.9867); Absent from gnomAD v4.1; Associated with Glutaric acidemia type 2A.

What condition is associated with ETFA p.Val263Gly (c.788T>G)?

ETFA p.Val263Gly (c.788T>G) is associated with Glutaric acidemia type 2A (ClinVar).

How common is ETFA p.Val263Gly (c.788T>G) in the general population?

ETFA p.Val263Gly (c.788T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ETFA p.Val263Gly (c.788T>G)?

AlphaMissense predicts likely pathogenic (score 0.9867) — an in-silico prediction, not a clinical call.

ETFA p.Val263Gly

c.788T>G · VCV4067432

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9867 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Glutaric acidemia type 2A

Computational evidence

Protein change
AlphaMissense	0.9867	likely pathogenic
REVEL	0.978	strongly pathogenic-leaning
SaProt	LLR -14.35	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.7, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 95 kb · p 0.0051 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ETFA
Protein: p.Val263Gly
Coding: c.788T>G
MANE Select: NM_000126
Type: single nucleotide variant
Location: chr15:76274440 (GRCh38)
Gene constraint: LOEUF 1.166 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.00 · 4 PDB
Residue 263: the 'domain ii' region; a binding site; a β-strand

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

Disease context

Glutaric acidemia type 2A

Similar variants

ETFA p.Arg122Lys Likely pathogenic ★★ same condition
ETFA p.Arg18Ter Pathogenic/Likely pathogenic ★★ same condition
ETFA p.Arg209Ter Pathogenic/Likely pathogenic ★★ same condition
ETFA p.Arg223Ter Pathogenic/Likely pathogenic ★★ same condition
ETFA p.Gln65Ter Likely pathogenic ★★ same condition
ETFA p.Gly116Arg Likely pathogenic ★★ same condition
ETFA p.Met1Ile Pathogenic/Likely pathogenic ★★ same condition
ETFA p.Met1Val Pathogenic ★★ same condition

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/etfa-p-val263gly (accessed [today's date]).

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