Is EEF1A2 p.Arg266Trp (c.796C>T) pathogenic?

EEF1A2 p.Arg266Trp (c.796C>T) is classified Pathogenic/Likely pathogenic in EEF1A2 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2022-08-16). AlphaMissense: likely pathogenic (0.9991); Absent from gnomAD v4.1; Associated with EEF1A2-related disorder.

What condition is associated with EEF1A2 p.Arg266Trp (c.796C>T)?

EEF1A2 p.Arg266Trp (c.796C>T) is associated with EEF1A2-related disorder, intellectual disability, autosomal dominant 38, developmental and epileptic encephalopathy, 33 (ClinVar).

How common is EEF1A2 p.Arg266Trp (c.796C>T) in the general population?

EEF1A2 p.Arg266Trp (c.796C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EEF1A2 p.Arg266Trp (c.796C>T)?

AlphaMissense predicts likely pathogenic (score 0.9991) — an in-silico prediction, not a clinical call.

EEF1A2 p.Arg266Trp

c.796C>T · rs1555883505 · VCV449242

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

AlphaMissense

likely pathogenic

0.9991 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,604,414)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

EEF1A2-related disorder

Computational evidence

Protein change
AlphaMissense	0.9991	likely pathogenic ✓ concordant with ClinVar
REVEL	0.634	indeterminate
SaProt	LLR -14.82	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 4.5	GERP -0.5, phastCons 1
Regional constraint	o/e 0.27	constrained · MANE · 4,822 bp · p 4e-36 · regional, not allelic
Overall
CADD	25.8	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

No allele count reported in gnomAD v4.1 (AN 1,604,414). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: EEF1A2
Protein: p.Arg266Trp
Coding: c.796C>T
MANE Select: NM_001958
dbSNP: rs1555883505
Type: single nucleotide variant
Location: chr20:63490712 (GRCh38)
Gene constraint: LOEUF 0.314 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 88.70 · 2 PDB
Residue 266: a β-strand

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

Disease context

EEF1A2-related disorder

Also linked: intellectual disability, autosomal dominant 38 developmental and epileptic encephalopathy, 33

Similar variants

EEF1A2 p.Arg266Gln Likely pathogenic ★★ same residue
EEF1A2 p.Arg423Cys Pathogenic/Likely pathogenic ★★ same condition
EEF1A2 p.Arg69Cys Pathogenic ★★ same condition
EEF1A2 p.Asp252Asn Pathogenic/Likely pathogenic ★★ ⚠ same condition
EEF1A2 p.Asp91Asn Pathogenic ★★ same condition
EEF1A2 p.Asp97Asn Pathogenic/Likely pathogenic ★★ same condition
EEF1A2 p.Glu122Lys Pathogenic/Likely pathogenic ★★ same condition
EEF1A2 p.Glu124Lys Pathogenic/Likely 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-arg266trp (accessed [today's date]).

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