RP2 p.Pro54=
c.162T>C · rs782744976 · VCV1925917
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00123%, nfe)
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 0.92 | GERP 0.53, phastCons 1 |
| Overall | ||
| CADD | 10.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00123%
European (non-Finnish) · 11/894,735 alleles
Filtering AF
0.00066%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000482%
Overall
0.00091%
11/1,209,283 alleles · very rare
exomes 8/1,097,505 · genomes 3/111,778 · joint denominator
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
- RP2
- Protein
- p.Pro54=
- Coding
- c.162T>C
- MANE Select
- NM_006915
- dbSNP
- rs782744976
- Type
- single nucleotide variant
- Location
- chrX:46853535 (GRCh38)
- Structure
- AlphaFold pLDDT 91.64 · 3 PDB
- Residue 54
- the c-cap/cofactor c-like domain
Similar variants
- RP2 p.Pro54Leu Uncertain significance ★ ⚠ same residue
- RP2 c.768+1G>T Pathogenic ★★ same type
- RP2 c.884-1G>A Pathogenic ★★ same type
- RP2 c.969+2T>C Pathogenic/Likely pathogenic ★★ same type
- RP2 c.969+3A>G Pathogenic ★★ same type
- RP2 p.Arg118Cys Pathogenic/Likely pathogenic ★★ same type
- RP2 p.Arg118His Pathogenic/Likely pathogenic ★★ same type
- RP2 p.Arg120Ter Pathogenic ★★ 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/rp2-p-pro54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown