RBP3 p.Pro580=
c.1740G>A · rs140857967 · VCV2981870
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
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 -4.6 | GERP -3 |
| Overall | ||
| CADD | 0.953 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,878 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.0018%
29/1,608,638 alleles · very rare
exomes 25/1,456,292 · genomes 4/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,959 |
| South Asian | 0.00439% | 22,769 |
| European (non-Finnish) | 0.00178% | 56,187 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,468 |
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.Pro580=
- Coding
- c.1740G>A
- MANE Select
- NM_002900
- dbSNP
- rs140857967
- Type
- single nucleotide variant
- Location
- chr10:47350224 (GRCh38)
- Structure
- AlphaFold pLDDT 63.40 · 8 PDB
Similar variants
- RBP3 p.Arg388Ter Pathogenic ★★ same type
- RBP3 p.Gln141Ter Pathogenic/Likely pathogenic ★★ same type
- RBP3 p.Gln54Ter Pathogenic ★★ same type
- RBP3 p.Glu149Ter Pathogenic ★★ same type
- RBP3 p.Glu692Ter Pathogenic/Likely pathogenic ★★ same type
- RBP3 p.Tyr784Ter Pathogenic/Likely pathogenic ★★ same type
- RBP3 p.Tyr841Ter Pathogenic/Likely pathogenic ★★ same type
- RBP3 c.3388+4C>G 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/rbp3-p-pro580 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown