RBFOX2 p.Asp89=
c.267C>T · VCV4750208
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0626%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 13.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0626%
South Asian · 57/91,080 alleles
Filtering AF
0.0496%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0449%
Overall
0.0057%
92/1,614,130 alleles · ultra-rare
exomes 85/1,461,890 · genomes 7/152,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0626% | 1,598 |
| Middle Eastern | 0.0165% | 6,060 |
| East Asian | 0.00446% | 22,443 |
| European (non-Finnish) | 0.00246% | 40,690 |
| Admixed American | 0.00167% | 60,014 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,504 |
| African / African-American | 0.00133% | 75,020 |
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
- RBFOX2
- Protein
- p.Asp89=
- Coding
- c.267C>T
- MANE Select
- NM_001349999
- Type
- single nucleotide variant
- Location
- chr22:35809975 (GRCh38)
- Gene constraint
- LOEUF 0.336 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 55.86 · 1 PDB
- Residue 89
- the 'disordered' region
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-asp89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown