Is RBFOX1 p.Pro290= (c.870C>T) pathogenic?

RBFOX1 p.Pro290= (c.870C>T) is classified Likely benign in RBFOX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-18). Very rare (popmax 0.0023%, eas); Associated with idiopathic generalized epilepsy.

What condition is associated with RBFOX1 p.Pro290= (c.870C>T)?

RBFOX1 p.Pro290= (c.870C>T) is associated with idiopathic generalized epilepsy (ClinVar).

How common is RBFOX1 p.Pro290= (c.870C>T) in the general population?

RBFOX1 p.Pro290= (c.870C>T) is very rare (popmax 0.0023%, eas) (gnomAD).

RBFOX1 p.Pro290=

c.870C>T · rs746553919 · VCV2712970

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0023%, eas)

Conditions

idiopathic generalized epilepsy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.5	GERP -1.4, phastCons 0.027
Overall
CADD	4.492	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0023% East Asian · 1/43,416 alleles

Filtering AF 0.000626% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000483%

Overall 0.0009% 14/1,555,414 alleles · very rare exomes 14/1,403,118 · genomes 0/152,296 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0023%	43,416
European (non-Finnish)	0.00112%	89,066

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: RBFOX1
Protein: p.Pro290=
Coding: c.870C>T
MANE Select: NM_018723
dbSNP: rs746553919
Type: single nucleotide variant
Location: chr16:7653927 (GRCh38)
Gene constraint: LOEUF 0.311 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 56.23 · 4 PDB

Full RBFOX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

idiopathic generalized epilepsy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

RBFOX1 p.Pro290Thr Uncertain significance ★ ⚠ same residue
RBFOX1 p.Pro290Ser Uncertain significance ★ ⚠ same residue
RBFOX1 p.Ala21Ser Uncertain significance ★★ same condition
RBFOX1 p.Ala21Val Uncertain significance ★★ same condition
RBFOX1 p.Ala225Thr Uncertain significance ★★ ⚠ same condition
RBFOX1 p.Ala264Thr Uncertain significance ★★ ⚠ same condition
RBFOX1 p.Ala315Thr Uncertain significance ★★ ⚠ same condition
RBFOX1 p.Arg317Cys 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/rbfox1-p-pro290 (accessed [today's date]).

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