RBP3 p.Ala619=
c.1857C>T · rs782455598 · VCV1535152
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00549%, sas)
Conditions
1
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 -15 | GERP -2.9 |
| Overall | ||
| CADD | 0.445 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00549%
South Asian · 5/91,088 alleles
Filtering AF
0.0021%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00136%
Overall
0.000372%
6/1,611,752 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00549% | 18,218 |
| East Asian | 0.00223% | 44,890 |
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.Ala619=
- Coding
- c.1857C>T
- MANE Select
- NM_005225 · reported on NM_002900
- dbSNP
- rs782455598
- Type
- single nucleotide variant
- Location
- chr10:47350341 (GRCh38)
- Structure
- AlphaFold pLDDT 63.40 · 8 PDB
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.Ala325Thr Uncertain significance ★★ ⚠ same condition
- RBP3 p.Ala546Val Uncertain significance ★★ ⚠ same condition
- RBP3 p.Ala570Val Uncertain significance ★★ ⚠ same condition
- RBP3 p.Ala803Thr Uncertain significance ★★ ⚠ same condition
- RBP3 p.Ala830Thr 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-ala619 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown