Is EEF1A2 p.Arg430Lys (c.1289G>A) pathogenic?

EEF1A2 p.Arg430Lys (c.1289G>A) is classified Uncertain significance in EEF1A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-23). AlphaMissense: likely pathogenic (0.7522); Absent from gnomAD v4.1.

How common is EEF1A2 p.Arg430Lys (c.1289G>A) in the general population?

EEF1A2 p.Arg430Lys (c.1289G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EEF1A2 p.Arg430Lys (c.1289G>A)?

AlphaMissense predicts likely pathogenic (score 0.7522) — an in-silico prediction, not a clinical call.

EEF1A2 p.Arg430Lys

c.1289G>A · rs1064796704 · VCV423928

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7522 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,474,180)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.7522	likely pathogenic
REVEL	0.187	benign-leaning
SaProt	LLR -9.42	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.7	GERP 0.58, phastCons 1
Regional constraint	o/e 0.54	unconstrained · MANE · 108 bp · p 0.00057 · regional, not allelic
Overall
CADD	24.1	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 1,474,180). 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.Arg430Lys
Coding: c.1289G>A
MANE Select: NM_001958
dbSNP: rs1064796704
Type: single nucleotide variant
Location: chr20:63488401 (GRCh38)
Gene constraint: LOEUF 0.314 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 88.70 · 2 PDB

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

Similar variants

EEF1A2 p.Arg266Gln Likely pathogenic ★★ same type
EEF1A2 p.Arg266Trp Pathogenic/Likely pathogenic ★★ same type
EEF1A2 p.Arg423Cys Pathogenic/Likely pathogenic ★★ same type
EEF1A2 p.Arg69Cys Pathogenic ★★ same type
EEF1A2 p.Asp252Asn Pathogenic/Likely pathogenic ★★ ⚠ same type
EEF1A2 p.Asp91Asn Pathogenic ★★ same type
EEF1A2 p.Asp97Asn Pathogenic/Likely pathogenic ★★ same type
EEF1A2 p.Glu122Lys Pathogenic/Likely pathogenic ★★ 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/eef1a2-p-arg430lys (accessed [today's date]).

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