Is EEF1A2 p.Glu413Asp (c.1239G>C) pathogenic?

EEF1A2 p.Glu413Asp (c.1239G>C) is classified Uncertain significance in EEF1A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-09). AlphaMissense: likely pathogenic (0.9894); Absent from gnomAD v4.1.

How common is EEF1A2 p.Glu413Asp (c.1239G>C) in the general population?

EEF1A2 p.Glu413Asp (c.1239G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EEF1A2 p.Glu413Asp (c.1239G>C)?

AlphaMissense predicts likely pathogenic (score 0.9894) — an in-silico prediction, not a clinical call.

EEF1A2 p.Glu413Asp

c.1239G>C · rs2082365938 · VCV3253023

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9894 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9894	likely pathogenic
REVEL	0.33	indeterminate
SaProt	LLR -9.15	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.32 · evaluated, not missing
Constraint at this position
Conservation	phyloP 5.9	GERP 0.71, phastCons 1
Regional constraint	o/e 0.27	constrained · MANE · 4,822 bp · p 4e-36 · regional, not allelic
Overall
CADD	25.2	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

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: EEF1A2
Protein: p.Glu413Asp
Coding: c.1239G>C
MANE Select: NM_001958
dbSNP: rs2082365938
Type: single nucleotide variant
Location: chr20:63488943 (GRCh38)
Gene constraint: LOEUF 0.314 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 88.70 · 2 PDB

Full EEF1A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EEF1A2 p.Arg266Gln Likely pathogenic ★★ same type
EEF1A2 p.Arg266Trp Pathogenic/Likely pathogenic ★★ same type
EEF1A2 p.Arg423Cys Pathogenic/Likely pathogenic ★★ same type
EEF1A2 p.Arg69Cys Pathogenic ★★ same type
EEF1A2 p.Asp252Asn Pathogenic/Likely pathogenic ★★ ⚠ same type
EEF1A2 p.Asp91Asn Pathogenic ★★ same type
EEF1A2 p.Asp97Asn Pathogenic/Likely pathogenic ★★ same type
EEF1A2 p.Glu122Lys 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/eef1a2-p-glu413asp (accessed [today's date]).

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