Is EEF1AKMT3 p.Asp73Val (c.218A>T) pathogenic?

EEF1AKMT3 p.Asp73Val (c.218A>T) is classified Uncertain significance in EEF1AKMT3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-08). AlphaMissense: likely benign (0.2475); Absent from gnomAD v4.1.

How common is EEF1AKMT3 p.Asp73Val (c.218A>T) in the general population?

EEF1AKMT3 p.Asp73Val (c.218A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EEF1AKMT3 p.Asp73Val (c.218A>T)?

AlphaMissense predicts likely benign (score 0.2475) — an in-silico prediction, not a clinical call.

EEF1AKMT3 p.Asp73Val

c.218A>T · rs2540932770 · VCV2617496

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2475 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2475	likely benign
REVEL	0.234	benign-leaning
SaProt	LLR -11.48	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	Δ0.21	donor loss, 16 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 11	GERP 1.5, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 7,918 bp · p 0.013 · regional, not allelic
Overall
CADD	31.0	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

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: EEF1AKMT3
Protein: p.Asp73Val
Coding: c.218A>T
MANE Select: NM_015433
dbSNP: rs2540932770
Type: single nucleotide variant
Location: chr12:57773057 (GRCh38)
Gene constraint: LOEUF 1.345 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.21 · 1 PDB

Full EEF1AKMT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EEF1AKMT3 p.Ala126Thr Uncertain significance ★ ⚠ same type
EEF1AKMT3 p.Ala130Gly Uncertain significance ★ ⚠ same type
EEF1AKMT3 p.Ala142Thr Uncertain significance ★ ⚠ same type
EEF1AKMT3 p.Ala54Gly Uncertain significance ★ ⚠ same type
EEF1AKMT3 p.Arg129Cys Uncertain significance ★ ⚠ same type
EEF1AKMT3 p.Arg207Trp Uncertain significance ★ ⚠ same type
EEF1AKMT3 p.Asn143Lys Uncertain significance ★ ⚠ same type
EEF1AKMT3 p.Asn65Ser 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/eef1akmt3-p-asp73val (accessed [today's date]).

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