PTPRM p.Asp45=
c.135C>T · rs148329685 · VCV722994
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.404%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 11.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.404%
African / African-American · 303/75,050 alleles
Filtering AF
0.366%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.352%
Overall
0.0201%
324/1,613,772 alleles · rare
exomes 147/1,461,462 · genomes 177/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.404% | 248 |
| Admixed American | 0.0183% | 5,457 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,944 |
| European (non-Finnish) | 8.48e-05% | 1,179,651 |
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
- PTPRM
- Protein
- p.Asp45=
- Coding
- c.135C>T
- MANE Select
- NM_001105244
- dbSNP
- rs148329685
- Type
- single nucleotide variant
- Location
- chr18:7774210 (GRCh38)
- Gene constraint
- LOEUF 0.334 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.38 · 5 PDB
- Residue 45
- a β-strand; the mam domain
Similar variants
- PTPRM c.664-9T>C Benign/Likely benign ★★ same type
- PTPRM p.Ala748= Benign ★★ same type
- PTPRM p.Ser39Arg Benign ★★ same type
- PTPRM p.Thr445= Benign ★★ same type
- PTPRM p.Val333= Benign ★★ same type
- PTPRM p.Ala1128Gly Uncertain significance ★ ⚠ same type
- PTPRM p.Ala1163Glu Uncertain significance ★ ⚠ same type
- PTPRM p.Ala1163Val 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/ptprm-p-asp45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown