RP2 p.Phe319=
c.957C>T · rs781970360 · VCV2977638
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0175%, amr)
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 4.8 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 13.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0175%
Admixed American · 8/45,608 alleles
Filtering AF
0.00871%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00632%
Overall
0.000685%
8/1,168,420 alleles · ultra-rare
exomes 6/1,056,706 · genomes 2/111,714 · 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.Phe319=
- Coding
- c.957C>T
- MANE Select
- NM_006915
- dbSNP
- rs781970360
- Type
- single nucleotide variant
- Location
- chrX:46877578 (GRCh38)
- Structure
- AlphaFold pLDDT 91.64 · 3 PDB
Similar variants
- RP2 p.Phe319Leu 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-phe319 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown