Is EEF1A2 p.Gln343Lys (c.1027C>A) pathogenic?

EEF1A2 p.Gln343Lys (c.1027C>A) is classified Likely pathogenic in EEF1A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-10). AlphaMissense: likely pathogenic (0.9918); Absent from gnomAD v4.1; Associated with intellectual disability, autosomal dominant 38.

What condition is associated with EEF1A2 p.Gln343Lys (c.1027C>A)?

EEF1A2 p.Gln343Lys (c.1027C>A) is associated with intellectual disability, autosomal dominant 38 (ClinVar).

How common is EEF1A2 p.Gln343Lys (c.1027C>A) in the general population?

EEF1A2 p.Gln343Lys (c.1027C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EEF1A2 p.Gln343Lys (c.1027C>A)?

AlphaMissense predicts likely pathogenic (score 0.9918) — an in-silico prediction, not a clinical call.

EEF1A2 p.Gln343Lys

c.1027C>A · VCV4277778

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9918 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

intellectual disability, autosomal dominant 38

Computational evidence

Protein change
AlphaMissense	0.9918	likely pathogenic ✓ concordant with ClinVar
REVEL	0.45	indeterminate
SaProt	LLR -14.11	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.27	constrained · MANE · 4,822 bp · p 4e-36 · regional, not allelic
Overall
CADD	26.8	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.Gln343Lys
Coding: c.1027C>A
MANE Select: NM_001958
Type: single nucleotide variant
Location: chr20:63490481 (GRCh38)
Gene constraint: LOEUF 0.314 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 88.70 · 2 PDB
Residue 343: a β-strand

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

Disease context

intellectual disability, autosomal dominant 38 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EEF1A2 p.Arg266Gln Likely pathogenic ★★ same condition
EEF1A2 p.Arg266Trp Pathogenic/Likely pathogenic ★★ same condition
EEF1A2 p.Asp91Asn Pathogenic ★★ same condition
EEF1A2 p.Glu122Lys Pathogenic/Likely pathogenic ★★ same condition
EEF1A2 p.Glu124Lys Pathogenic/Likely pathogenic ★★ same condition
EEF1A2 p.Gly70Ser Pathogenic ★★ same condition
EEF1A2 p.Thr432Met Pathogenic/Likely pathogenic ★★ same condition
EEF1A2 p.Arg218His Uncertain significance ★★ ⚠ 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/eef1a2-p-gln343lys (accessed [today's date]).

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