PTPRS p.Val697=
c.2091C>T · rs79957927 · VCV777382
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.1%, afr)
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 0.004 | GERP -3.5 |
| Overall | ||
| CADD | 13.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.1%
African / African-American · 824/74,958 alleles
Filtering AF
1.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.01%
Overall
0.0576%
929/1,612,852 alleles · low-frequency
exomes 472/1,460,786 · genomes 457/152,066 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.1% | 91 |
| Remaining individualsnot grpmax-eligible | 0.0704% | 1,420 |
| Admixed American | 0.0517% | 1,936 |
| European (non-Finnish) | 0.00246% | 40,687 |
| South Asian | 0.0011% | 91,056 |
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.Val697=
- Coding
- c.2091C>T
- MANE Select
- NM_002850
- dbSNP
- rs79957927
- Type
- single nucleotide variant
- Location
- chr19:5231374 (GRCh38)
- Gene constraint
- LOEUF 0.378 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.94 · 6 PDB
- Residue 697
- the fibronectin type-iii 4 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-val697 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown