RBP3 p.Ala309=
c.927C>T · rs75452094 · VCV299993
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, eas)
Conditions
2
inherited retinal dystrophy
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 -20 | GERP -3 |
| Overall | ||
| CADD | 0.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
East Asian · 562/44,868 alleles
Filtering AF
1.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.13%
Overall
0.058%
935/1,611,882 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.25% | 80 |
| Remaining individualsnot grpmax-eligible | 0.256% | 390 |
| South Asian | 0.0692% | 1,446 |
| Admixed American | 0.0517% | 1,936 |
| European (non-Finnish) | 0.00975% | 10,261 |
| African / African-American | 0.004% | 25,008 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,592 |
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
- RBP3
- Protein
- p.Ala309=
- Coding
- c.927C>T
- MANE Select
- NM_005225 · reported on NM_002900
- dbSNP
- rs75452094
- Type
- single nucleotide variant
- Location
- chr10:47349411 (GRCh38)
- Structure
- AlphaFold pLDDT 63.40 · 8 PDB
- Residue 309
- the 'required for interaction with trim28' region; the 'disordered' region
Similar variants
- RBP3 p.Gln141Ter Pathogenic/Likely pathogenic ★★ same condition
- RBP3 p.Glu149Ter Pathogenic ★★ same condition
- RBP3 p.Ala263Ser Uncertain significance ★★ ⚠ same condition
- RBP3 p.Ala312Thr Uncertain significance ★★ same condition
- RBP3 p.Ala325Thr Uncertain significance ★★ ⚠ same condition
- RBP3 p.Ala379Thr Uncertain significance ★★ ⚠ same condition
- RBP3 p.Ala403Thr Uncertain significance ★★ ⚠ same condition
- RBP3 p.Ala546Val 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/rbp3-p-ala309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown