S1PR2 p.Pro285=
c.855C>T · rs202092003 · VCV1210576
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0624%, 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 -8.2 | GERP -5.1 |
| Overall | ||
| CADD | 0.157 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0624%
East Asian · 28/44,890 alleles
Filtering AF
0.0443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0382%
Overall
0.00528%
85/1,610,956 alleles · ultra-rare
exomes 76/1,458,584 · genomes 9/152,372 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0624% | 1,603 |
| European (non-Finnish) | 0.00432% | 23,138 |
| African / African-American | 0.004% | 25,023 |
| Admixed American | 0.00333% | 30,013 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,500 |
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
- S1PR2
- Protein
- p.Pro285=
- Coding
- c.855C>T
- MANE Select
- NM_004230
- dbSNP
- rs202092003
- Type
- single nucleotide variant
- Location
- chr19:10224051 (GRCh38)
- Gene constraint
- LOEUF 0.834 · pLI 0.06 (gnomAD)
- Structure
- AlphaFold pLDDT 82.73 · 2 PDB
- Residue 285
- an α-helix
Similar variants
- S1PR2 p.Ala36Val Uncertain significance ★★ ⚠ same type
- S1PR2 p.Ala77Thr Uncertain significance ★★ ⚠ same type
- S1PR2 p.Ala77Val Uncertain significance ★★ ⚠ same type
- S1PR2 p.Arg211His Uncertain significance ★★ ⚠ same type
- S1PR2 p.Arg217His Uncertain significance ★★ ⚠ same type
- S1PR2 p.Arg293Trp Uncertain significance ★★ ⚠ same type
- S1PR2 p.Arg297Trp Uncertain significance ★★ ⚠ same type
- S1PR2 p.Arg315Gln 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/s1pr2-p-pro285 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown