Is EEF1A1 p.Cys31Trp (c.93C>G) pathogenic?

EEF1A1 p.Cys31Trp (c.93C>G) is classified Uncertain significance in EEF1A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-26). AlphaMissense: likely pathogenic (0.9984); Absent from gnomAD v4.1.

How common is EEF1A1 p.Cys31Trp (c.93C>G) in the general population?

EEF1A1 p.Cys31Trp (c.93C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EEF1A1 p.Cys31Trp (c.93C>G)?

AlphaMissense predicts likely pathogenic (score 0.9984) — an in-silico prediction, not a clinical call.

EEF1A1 p.Cys31Trp

c.93C>G · rs778266425 · VCV2672187

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9984 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9984	likely pathogenic
REVEL	0.617	indeterminate
SaProt	LLR -15.04	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 -0.13	GERP -4.8, phastCons 0.003
Regional constraint	o/e 0.25	constrained · MANE · 1,032 bp · p 9.3e-30 · regional, not allelic
Overall
CADD	18.95	PHRED · no single calibrated threshold — expert panels disagree

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

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: EEF1A1
Protein: p.Cys31Trp
Coding: c.93C>G
MANE Select: NM_001402
dbSNP: rs778266425
Type: single nucleotide variant
Location: chr6:73519934 (GRCh38)
Gene constraint: LOEUF 0.126 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 88.06 · 14 PDB
Residue 31: the tr-type g domain

Full EEF1A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MTO1 p.Gln595= Benign/Likely benign ★★ same type
EEF1A1 p.Ala448Ser Uncertain significance ★ ⚠ same type
EEF1A1 p.Arg321His Uncertain significance ★ ⚠ same type
EEF1A1 p.Arg96Thr Uncertain significance ★ ⚠ same type
EEF1A1 p.Asn331His Uncertain significance ★ ⚠ same type
EEF1A1 p.Asp389Asn Uncertain significance ★ ⚠ same type
EEF1A1 p.Gly151Ser Uncertain significance ★ ⚠ same type
EEF1A1 p.Ile235Val 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/eef1a1-p-cys31trp (accessed [today's date]).

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