PTPRO p.His213=
c.639C>T · rs142711597 · VCV2085274
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.292%, 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 -1.8 | GERP -5.3 |
| Overall | ||
| CADD | 8.159 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.292%
African / African-American · 219/74,992 alleles
Filtering AF
0.26%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.248%
Overall
0.0222%
358/1,613,696 alleles · rare
exomes 196/1,461,536 · genomes 162/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.292% | 342 |
| Admixed American | 0.102% | 984 |
| Remaining individualsnot grpmax-eligible | 0.0352% | 2,840 |
| Middle Eastern | 0.033% | 3,029 |
| East Asian | 0.00669% | 14,945 |
| South Asian | 0.00439% | 22,765 |
| European (non-Finnish) | 0.00398% | 25,101 |
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.His213=
- Coding
- c.639C>T
- MANE Select
- NM_030667
- dbSNP
- rs142711597
- Type
- single nucleotide variant
- Location
- chr12:15499572 (GRCh38)
- Gene constraint
- LOEUF 0.513 · pLI 0.17 (gnomAD)
- Structure
- AlphaFold pLDDT 77.55 · 2 PDB
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-his213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown