PTPRB p.Leu601Pro
c.1802T>C · VCV3427962
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00271%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.656 | pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.6, phastCons 1 |
| Regional constraint | o/e 0.94 | unconstrained · MANE · 66 kb · p 0.021 · regional, not allelic |
| Overall | ||
| CADD | 27.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00271%
African / African-American · 2/73,718 alleles
Filtering AF
0.00045%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000169%
Overall
0.000254%
4/1,572,350 alleles · very rare
exomes 2/1,420,132 · genomes 2/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00271% | 36,859 |
| European (non-Finnish) | 0.000173% | 578,992 |
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
- PTPRB
- Protein
- p.Leu601Pro
- Coding
- c.1802T>C
- MANE Select
- NM_001109754
- Type
- single nucleotide variant
- Location
- chr12:70590212 (GRCh38)
- Gene constraint
- LOEUF 0.466 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 80.67 · 14 PDB
- Residue 601
- the fibronectin type-iii 7 domain
Similar variants
- PTPRB c.3370+4A>G Benign ★★ same type
- PTPRB p.Ala1520= Benign ★★ same type
- PTPRB p.Leu1142= Benign ★★ same type
- PTPRB p.Pro1816= Benign/Likely benign ★★ same type
- PTPRB p.Thr1699= Benign ★★ same type
- PTPRB p.Ala1027Ser Uncertain significance ★ same type
- PTPRB p.Ala1088Thr Uncertain significance ★ same type
- PTPRB p.Ala1117Val 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/ptprb-p-leu601pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown