PTPRM p.Val882=
c.2646G>A · rs78499397 · VCV3042788
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.57%, afr)
Conditions
1
PTPRM-related disorder
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 1.9 | GERP -0.6, phastCons 1 |
| Overall | ||
| CADD | 4.874 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.57%
African / African-American · 1,162/74,176 alleles
Filtering AF
1.49%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.46%
Overall
0.0799%
1,277/1,599,052 alleles · low-frequency
exomes 605/1,446,796 · genomes 672/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.57% | 64 |
| Remaining individualsnot grpmax-eligible | 0.0855% | 1,169 |
| Admixed American | 0.0809% | 1,236 |
| Middle Eastern | 0.0663% | 1,509 |
| South Asian | 0.00339% | 29,455 |
| European (non-Finnish) | 0.000682% | 146,617 |
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.Val882=
- Coding
- c.2646G>A
- MANE Select
- NM_001105244
- dbSNP
- rs78499397
- Type
- single nucleotide variant
- Location
- chr18:8253306 (GRCh38)
- Gene constraint
- LOEUF 0.334 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.38 · 5 PDB
- Residue 882
- a turn
Disease context
PTPRM-related disorder
Similar variants
- PTPRM p.Val882Met Uncertain significance ★ ⚠ same residue
- PTPRM p.Phe1069Leu Uncertain significance ⚠ same condition
- PTPRM c.1754-6C>T Likely benign same condition
- PTPRM c.3462+9G>A Likely benign same condition
- PTPRM c.4045-5C>T Benign same condition
- PTPRM c.839-7C>G Likely benign same condition
- PTPRM p.Ala198= Likely benign same condition
- PTPRM p.Ala673= Likely benign same condition
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-val882 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown