Is EEF1A2 p.Arg96Cys (c.286C>T) pathogenic?

EEF1A2 p.Arg96Cys (c.286C>T) is classified Pathogenic in EEF1A2 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-09-18). AlphaMissense: likely pathogenic (0.9986); Absent from gnomAD v4.1; Associated with intellectual disability, autosomal dominant 38.

What condition is associated with EEF1A2 p.Arg96Cys (c.286C>T)?

EEF1A2 p.Arg96Cys (c.286C>T) is associated with intellectual disability, autosomal dominant 38 (ClinVar).

How common is EEF1A2 p.Arg96Cys (c.286C>T) in the general population?

EEF1A2 p.Arg96Cys (c.286C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EEF1A2 p.Arg96Cys (c.286C>T)?

AlphaMissense predicts likely pathogenic (score 0.9986) — an in-silico prediction, not a clinical call.

EEF1A2 p.Arg96Cys

c.286C>T · rs865888375 · VCV2664000

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9986 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

intellectual disability, autosomal dominant 38

Computational evidence

Protein change
AlphaMissense	0.9986	likely pathogenic ✓ concordant with ClinVar
REVEL	0.79	moderately pathogenic-leaning
SaProt	LLR -14.07	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 2.3	GERP -3.8, phastCons 1
Regional constraint	o/e 0.18	constrained · MANE · 2,668 bp · p 1.1e-24 · regional, not allelic
Overall
CADD	24.3	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.Arg96Cys
Coding: c.286C>T
MANE Select: NM_001958
dbSNP: rs865888375
Type: single nucleotide variant
Location: chr20:63495894 (GRCh38)
Gene constraint: LOEUF 0.314 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 88.70 · 2 PDB
Residue 96: the tr-type g domain

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.Arg96= Likely benign ★ same residue
EEF1A2 p.Arg96His Likely pathogenic same residue
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

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-arg96cys (accessed [today's date]).

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