Is EIF3F p.Ile263Val (c.787A>G) pathogenic?

EIF3F p.Ile263Val (c.787A>G) is classified Uncertain significance in EIF3F (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-06). AlphaMissense: likely benign (0.0973); Very rare (popmax 0.00167%, amr); Associated with Inborn genetic diseases.

What condition is associated with EIF3F p.Ile263Val (c.787A>G)?

EIF3F p.Ile263Val (c.787A>G) is associated with Inborn genetic diseases (ClinVar).

How common is EIF3F p.Ile263Val (c.787A>G) in the general population?

EIF3F p.Ile263Val (c.787A>G) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about EIF3F p.Ile263Val (c.787A>G)?

AlphaMissense predicts likely benign (score 0.0973) — an in-silico prediction, not a clinical call.

EIF3F p.Ile263Val

c.787A>G · rs1387529492 · VCV2558128

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0973 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0973	likely benign
REVEL	0.037	moderately benign-leaning
SaProt	LLR -5.21	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.3	GERP 1.9, phastCons 1
Regional constraint	o/e 0.75	unconstrained · MANE · 8,406 bp · p 4.6e-06 · regional, not allelic
Overall
CADD	17.84	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.00167% Admixed American · 1/59,994 alleles

Overall 0.000186% 3/1,613,742 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,994
African / African-American	0.00134%	74,900
European (non-Finnish)	8.48e-05%	1,179,883

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: EIF3F
Protein: p.Ile263Val
Coding: c.787A>G
MANE Select: NM_003754
dbSNP: rs1387529492
Type: single nucleotide variant
Location: chr11:7995023 (GRCh38)
Gene constraint: LOEUF 0.46 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 75.97 · 29 PDB

Full EIF3F 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

EIF3F p.Asp292Glu Uncertain significance ★★ ⚠ same condition
EIF3F p.Pro7Ser Likely benign ★★ ⚠ same condition
EIF3F c.365-3C>T Uncertain significance ★ same condition
EIF3F p.Ala300Thr Uncertain significance ★ ⚠ same condition
EIF3F p.Ala44Val Uncertain significance ★ ⚠ same condition
EIF3F p.Ala51Gly Uncertain significance ★ ⚠ same condition
EIF3F p.Ala81Gly Uncertain significance ★ ⚠ same condition
EIF3F p.Arg192Gln Uncertain significance ★ ⚠ 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/eif3f-p-ile263val (accessed [today's date]).

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