Is EEF2 p.Val589Met (c.1765G>A) pathogenic?

EEF2 p.Val589Met (c.1765G>A) is classified Uncertain significance in EEF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-24). AlphaMissense: likely benign (0.1131); Very rare (popmax 0.00416%, afr).

How common is EEF2 p.Val589Met (c.1765G>A) in the general population?

EEF2 p.Val589Met (c.1765G>A) is very rare (popmax 0.00416%, afr) (gnomAD).

What do computational predictors say about EEF2 p.Val589Met (c.1765G>A)?

AlphaMissense predicts likely benign (score 0.1131) — an in-silico prediction, not a clinical call.

EEF2 p.Val589Met

c.1765G>A · rs35987350 · VCV1940529

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1131 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00416%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1131	likely benign
REVEL	0.074	moderately benign-leaning
SaProt	LLR -7.54	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 2.4, phastCons 1
Regional constraint	o/e 0.71	unconstrained · MANE · 1,578 bp · p 7.1e-09 · regional, not allelic
Overall
CADD	21.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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

Grpmax group 0.00416% African / African-American · 3/72,114 alleles

Filtering AF 0.00199% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00173%

Overall 0.00246% 37/1,501,258 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00416%	24,038
European (non-Finnish)	0.00278%	36,031
South Asian	0.00263%	38,018
Remaining individualsnot grpmax-eligible	0.00173%	57,840

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: EEF2
Protein: p.Val589Met
Coding: c.1765G>A
MANE Select: NM_001961
dbSNP: rs35987350
Type: single nucleotide variant
Location: chr19:3978121 (GRCh38)
Gene constraint: LOEUF 0.39 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 89.97 · 26 PDB

Full EEF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EEF2 p.Val589Ala Uncertain significance ★ ⚠ same residue
EEF2 p.Val589= Likely benign ★ same residue
EEF2 p.Ala237Thr Uncertain significance ★★ ⚠ same type
EEF2 p.Ala238Thr Uncertain significance ★★ ⚠ same type
EEF2 p.Ala338Gly Uncertain significance ★★ ⚠ same type
EEF2 p.Ala624Thr Uncertain significance ★★ ⚠ same type
EEF2 p.Ala808Val Uncertain significance ★★ ⚠ same type
EEF2 p.Arg633His Uncertain significance ★★ ⚠ 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/eef2-p-val589met (accessed [today's date]).

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