Is EEF1A2 p.Ala117Val (c.350C>T) pathogenic?

EEF1A2 p.Ala117Val (c.350C>T) is classified Uncertain significance in EEF1A2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-07-09). AlphaMissense: likely pathogenic (0.9976); Very rare (popmax 8.48e-05%, nfe); Associated with Inborn genetic diseases.

What condition is associated with EEF1A2 p.Ala117Val (c.350C>T)?

EEF1A2 p.Ala117Val (c.350C>T) is associated with Inborn genetic diseases (ClinVar).

How common is EEF1A2 p.Ala117Val (c.350C>T) in the general population?

EEF1A2 p.Ala117Val (c.350C>T) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

What do computational predictors say about EEF1A2 p.Ala117Val (c.350C>T)?

AlphaMissense predicts likely pathogenic (score 0.9976) — an in-silico prediction, not a clinical call.

EEF1A2 p.Ala117Val

c.350C>T · rs866429985 · VCV589865

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9976 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9976	likely pathogenic
REVEL	0.624	indeterminate
SaProt	LLR -13.22	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 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.46	unconstrained · MANE · 1,861 bp · p 1.2e-12 · regional, not allelic
Overall
CADD	29.8	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

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,824 alleles

Overall 0.000206% 3/1,459,004 alleles · very rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,566
Finnishnot grpmax-eligible	0.00163%	61,506
European (non-Finnish)grpmax	8.48e-05%	1,179,824

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: EEF1A2
Protein: p.Ala117Val
Coding: c.350C>T
MANE Select: NM_001958
dbSNP: rs866429985
Type: single nucleotide variant
Location: chr20:63495076 (GRCh38)
Gene constraint: LOEUF 0.314 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 88.70 · 2 PDB
Residue 117: the tr-type g domain; a β-strand

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EEF1A2 p.Ala117= Benign/Likely benign ★★ same residue
EEF1A2 p.Arg247Cys Uncertain significance ★★ ⚠ same condition
EEF1A2 p.Gly397Glu Uncertain significance ★★ ⚠ same condition
EEF1A2 p.Lys179Arg Uncertain significance ★★ ⚠ same condition
EEF1A2 p.Val150Met Uncertain significance ★★ ⚠ same condition
EEF1A2 p.Ala125= Benign/Likely benign ★★ same condition
EEF1A2 p.Arg423= Likely benign ★★ same condition
EEF1A2 p.Asn440= Benign/Likely benign ★★ 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-ala117val (accessed [today's date]).

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