Is EEF2 p.Arg601Trp (c.1801C>T) pathogenic?

EEF2 p.Arg601Trp (c.1801C>T) is classified Uncertain significance in EEF2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-06-06). AlphaMissense: likely pathogenic (0.9979); Absent from gnomAD v4.1; Associated with EEF2-related disorder.

What condition is associated with EEF2 p.Arg601Trp (c.1801C>T)?

EEF2 p.Arg601Trp (c.1801C>T) is associated with EEF2-related disorder (ClinVar).

How common is EEF2 p.Arg601Trp (c.1801C>T) in the general population?

EEF2 p.Arg601Trp (c.1801C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EEF2 p.Arg601Trp (c.1801C>T)?

AlphaMissense predicts likely pathogenic (score 0.9979) — an in-silico prediction, not a clinical call.

EEF2 p.Arg601Trp

c.1801C>T · VCV3345427

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9979 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,546,388)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

EEF2-related disorder

Computational evidence

Protein change
AlphaMissense	0.9979	likely pathogenic
REVEL	0.453	indeterminate
SaProt	LLR -15.57	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 2.9	GERP -1.1, phastCons 1
Regional constraint	o/e 0.71	unconstrained · MANE · 1,578 bp · p 7.1e-09 · regional, not allelic
Overall
CADD	27.4	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

No allele count reported in gnomAD v4.1 (AN 1,546,388). 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: EEF2
Protein: p.Arg601Trp
Coding: c.1801C>T
MANE Select: NM_001961
Type: single nucleotide variant
Location: chr19:3978085 (GRCh38)
Gene constraint: LOEUF 0.39 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 89.97 · 26 PDB
Residue 601: a β-strand

Full EEF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EEF2-related disorder

Similar variants

EEF2 p.Glu563Asp Uncertain significance ★ ⚠ same condition
EEF2 p.Glu742Ter Uncertain significance ★ same condition
EEF2 p.Gly347Arg Uncertain significance ★ ⚠ same condition
EEF2 p.Thr657= Likely benign same condition
EEF2 p.Gln670fs Likely pathogenic ★ same condition
EEF2 p.Ala237Thr Uncertain significance ★★ ⚠ same type
EEF2 p.Ala238Thr Uncertain significance ★★ ⚠ same type
EEF2 p.Ala338Gly 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/eef2-p-arg601trp (accessed [today's date]).

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