RBP3 p.Ile780=
c.2340C>T · rs782527628 · VCV1971745
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0423%, eas)
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 -5.9 | GERP -2.9 |
| Overall | ||
| CADD | 0.198 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0423%
East Asian · 19/44,896 alleles
Filtering AF
0.0276%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.023%
Overall
0.00167%
27/1,612,902 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0423% | 2,363 |
| South Asian | 0.00329% | 30,361 |
| European (non-Finnish) | 0.000424% | 236,004 |
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.Ile780=
- Coding
- c.2340C>T
- MANE Select
- NM_005225 · reported on NM_002900
- dbSNP
- rs782527628
- Type
- single nucleotide variant
- Location
- chr10:47350824 (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-ile780 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown