PTPRS p.Pro95=
c.285G>A · rs61757815 · VCV781422
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 10.1%, afr) — too common for a highly-penetrant pathogenic allele
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 -12 | GERP -3.5 |
| Overall | ||
| CADD | 1.581 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.1%
African / African-American · 7,581/74,986 alleles
Filtering AF
9.92%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.84%
Overall
0.541%
8,740/1,614,092 alleles · common
exomes 4,495/1,461,888 · genomes 4,245/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 10.1% | 10 |
| Middle Eastern | 0.907% | 110 |
| Remaining individualsnot grpmax-eligible | 0.683% | 146 |
| Admixed American | 0.595% | 168 |
| European (non-Finnish) | 0.0256% | 3,907 |
| South Asian | 0.0176% | 5,692 |
| East Asian | 0.00223% | 44,872 |
| Finnishnot grpmax-eligible | 0.00156% | 64,040 |
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
- PTPRS
- Protein
- p.Pro95=
- Coding
- c.285G>A
- MANE Select
- NM_002850
- dbSNP
- rs61757815
- Type
- single nucleotide variant
- Location
- chr19:5273536 (GRCh38)
- Gene constraint
- LOEUF 0.378 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.94 · 6 PDB
- Residue 95
- the ig-like c2-type 1 domain
Similar variants
- PTPRS p.Arg1572Trp Uncertain significance ★★ ⚠ same type
- PTPRS p.Ala87= Benign ★★ same type
- PTPRS p.Ala972= Benign ★★ same type
- PTPRS p.Asn1737= Benign ★★ same type
- PTPRS p.Glu165= Likely benign ★★ same type
- PTPRS p.Gly1107= Likely benign ★★ same type
- PTPRS p.His1642= Benign ★★ same type
- PTPRS p.Ile1741= Benign ★★ 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/ptprs-p-pro95 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown