Is EFTUD2 p.Val255Met (c.763G>A) pathogenic?

EFTUD2 p.Val255Met (c.763G>A) is classified Uncertain significance in EFTUD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-04). AlphaMissense: likely benign (0.3338); Very rare (popmax 0.00223%, eas).

How common is EFTUD2 p.Val255Met (c.763G>A) in the general population?

EFTUD2 p.Val255Met (c.763G>A) is very rare (popmax 0.00223%, eas) (gnomAD).

What do computational predictors say about EFTUD2 p.Val255Met (c.763G>A)?

AlphaMissense predicts likely benign (score 0.3338) — an in-silico prediction, not a clinical call.

EFTUD2 p.Val255Met

c.763G>A · rs2050941796 · VCV2008257

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3338 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.3338	likely benign
REVEL	0.503	indeterminate
SaProt	LLR -10.62	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.6, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 19 kb · p 1.7e-08 · regional, not allelic
Overall
CADD	26.6	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,886 alleles

Overall 0.000124% 2/1,614,052 alleles · very rare exomes 2/1,461,770 · genomes 0/152,282 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,886
European (non-Finnish)	8.47e-05%	1,179,990

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: EFTUD2
Protein: p.Val255Met
Coding: c.763G>A
MANE Select: NM_004247
dbSNP: rs2050941796
Type: single nucleotide variant
Location: chr17:44876040 (GRCh38)
Gene constraint: LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 89.94 · 72 PDB
Residue 255: the tr-type g domain; a β-strand

Full EFTUD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EFTUD2 p.Val255= Likely benign ★ same residue
EFTUD2 c.1058+1G>A Pathogenic ★★ same type
EFTUD2 c.1414-2A>G Pathogenic/Likely pathogenic ★★ same type
EFTUD2 c.1607+1G>T Likely pathogenic ★★ same type
EFTUD2 c.1962+1G>A Pathogenic/Likely pathogenic ★★ same type
EFTUD2 c.2133-2A>G Pathogenic/Likely pathogenic ★★ same type
EFTUD2 c.2562-2A>G Pathogenic/Likely pathogenic ★★ same type
EFTUD2 c.702+1G>T Pathogenic/Likely pathogenic ★★ same type

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/eftud2-p-val255met (accessed [today's date]).

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