PTPRO p.Phe752=
c.2256T>C · rs36020879 · VCV710130
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.42%, 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 -4.5 | GERP -3.8 |
| Overall | ||
| CADD | 7.792 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.42%
African / African-American · 1,067/75,040 alleles
Filtering AF
1.35%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.32%
Overall
0.0732%
1,182/1,614,002 alleles · low-frequency
exomes 539/1,461,672 · genomes 643/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.42% | 70 |
| Remaining individualsnot grpmax-eligible | 0.0992% | 1,008 |
| Admixed American | 0.0683% | 1,464 |
| Middle Eastern | 0.033% | 3,030 |
| South Asian | 0.00439% | 22,770 |
| European (non-Finnish) | 0.000508% | 196,657 |
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
- PTPRO
- Protein
- p.Phe752=
- Coding
- c.2256T>C
- MANE Select
- NM_030667
- dbSNP
- rs36020879
- Type
- single nucleotide variant
- Location
- chr12:15546660 (GRCh38)
- Gene constraint
- LOEUF 0.513 · pLI 0.17 (gnomAD)
- Structure
- AlphaFold pLDDT 77.55 · 2 PDB
- Residue 752
- the fibronectin type-iii 8 domain
Similar variants
- PTPRO p.Ala1086Val Uncertain significance ★★ ⚠ same type
- PTPRO p.Ala591Thr Uncertain significance ★★ ⚠ same type
- PTPRO p.Arg480Trp Uncertain significance ★★ same type
- PTPRO p.Arg607Gln Uncertain significance ★★ ⚠ same type
- PTPRO p.Asn569Asp Uncertain significance ★★ ⚠ same type
- PTPRO p.Asp162Val Uncertain significance ★★ ⚠ same type
- PTPRO p.Asp301His Uncertain significance ★★ ⚠ same type
- PTPRO p.Asp799Gly 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/ptpro-p-phe752 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown