Is RBFOX2 p.Pro102Ser (c.304C>T) pathogenic?

RBFOX2 p.Pro102Ser (c.304C>T) is classified Uncertain significance in RBFOX2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-11). Absent from gnomAD v4.1.

How common is RBFOX2 p.Pro102Ser (c.304C>T) in the general population?

RBFOX2 p.Pro102Ser (c.304C>T) is absent from gnomAD v4.1 (gnomAD).

RBFOX2 p.Pro102Ser

c.304C>T · rs2148140331 · VCV1374670

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.373	indeterminate
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1
Overall
CADD	29.2	PHRED · no single calibrated threshold — expert panels disagree

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: RBFOX2
Protein: p.Pro102Ser
Coding: c.304C>T
MANE Select: NM_001349999
dbSNP: rs2148140331
Type: single nucleotide variant
Location: chr22:35809938 (GRCh38)
Gene constraint: LOEUF 0.336 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 55.86 · 1 PDB
Residue 102: the 'disordered' region

Full RBFOX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RBFOX2 p.Asp417Asn Uncertain significance ★★ same type
RBFOX2 p.Asp41His Uncertain significance ★★ same type
RBFOX2 p.Glu229Gln Uncertain significance ★★ same type
RBFOX2 p.Gly133Arg Uncertain significance ★★ same type
RBFOX2 p.Gly409Ser Uncertain significance ★★ same type
RBFOX2 p.Met91Val Uncertain significance ★★ same type
RBFOX2 p.Pro104Leu Uncertain significance ★★ same type
RBFOX2 p.Pro307Ser 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/rbfox2-p-pro102ser (accessed [today's date]).

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