S1PR2 p.Asp294=
c.882C>T · rs35493500 · VCV732065
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.36%, 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 3.3 | GERP -4, phastCons 1 |
| Overall | ||
| CADD | 7.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.36%
East Asian · 611/44,876 alleles
Filtering AF
1.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.24%
Overall
0.0401%
646/1,612,616 alleles · low-frequency
exomes 628/1,460,242 · genomes 18/152,374 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.36% | 73 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,943 |
| European (non-Finnish) | 0.00203% | 49,154 |
| Admixed American | 0.00167% | 60,010 |
| Finnishnot grpmax-eligible | 0.00159% | 62,830 |
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.Asp294=
- Coding
- c.882C>T
- MANE Select
- NM_004230
- dbSNP
- rs35493500
- Type
- single nucleotide variant
- Location
- chr19:10224024 (GRCh38)
- Gene constraint
- LOEUF 0.834 · pLI 0.06 (gnomAD)
- Structure
- AlphaFold pLDDT 82.73 · 2 PDB
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-asp294 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown