Is EIF6 p.Ala51= (c.153G>A) pathogenic?

EIF6 p.Ala51= (c.153G>A) is classified Likely benign in EIF6 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-26). Very rare (popmax 6.88e-05%).

How common is EIF6 p.Ala51= (c.153G>A) in the general population?

EIF6 p.Ala51= (c.153G>A) is very rare (popmax 6.88e-05%) (gnomAD).

EIF6 p.Ala51=

c.153G>A · VCV4663747

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 6.88e-05%)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.446	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.2	GERP -5
Overall
CADD	9.857	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.88e-05%

Overall 6.88e-05% 1/1,452,690 alleles · very rare

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: EIF6
Protein: p.Ala51=
Coding: c.153G>A
MANE Select: NM_002212
Type: single nucleotide variant
Location: chr20:35284216 (GRCh38)
Gene constraint: LOEUF 0.623 · pLI 0.65 (gnomAD)
Structure: AlphaFold pLDDT 91.12 · 48 PDB
Residue 51: a β-strand

Full EIF6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EIF6 p.Ala183Thr Uncertain significance ★ ⚠ same type
EIF6 p.Arg100Gln Uncertain significance ★ ⚠ same type
EIF6 p.Arg85Cys Uncertain significance ★ ⚠ same type
EIF6 p.Arg85His Uncertain significance ★ ⚠ same type
EIF6 p.Asn156Ser Uncertain significance ★ ⚠ same type
EIF6 p.Asn9Thr Uncertain significance ★ ⚠ same type
EIF6 p.Asp144Asn Uncertain significance ★ ⚠ same type
EIF6 p.Asp78Asn 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/eif6-p-ala51 (accessed [today's date]).

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