PTPRO p.Asn236=
c.708C>T · rs1465926140 · VCV2955243
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 2.5 | GERP 0.79, phastCons 1 |
| Overall | ||
| CADD | 7.691 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,060 alleles
Overall
6.2e-05%
1/1,613,872 alleles · ultra-rare
exomes 1/1,461,682 · genomes 0/152,190 · joint denominator
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.Asn236=
- Coding
- c.708C>T
- MANE Select
- NM_030667
- dbSNP
- rs1465926140
- Type
- single nucleotide variant
- Location
- chr12:15501666 (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-asn236 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown