PTPRM p.Pro1304=
c.3912T>C · rs3744983 · VCV3053401
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.09%, eas)
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 -4.6 | GERP -3.7 |
| Overall | ||
| CADD | 0.725 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.09%
East Asian · 488/44,888 alleles
Filtering AF
1.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.976%
Overall
0.0325%
525/1,614,216 alleles · low-frequency
exomes 462/1,461,868 · genomes 63/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.09% | 92 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,125 |
| South Asian | 0.00878% | 11,385 |
| Admixed American | 0.00666% | 15,006 |
| European (non-Finnish) | 0.000424% | 236,007 |
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.Pro1304=
- Coding
- c.3912T>C
- MANE Select
- NM_001105244
- dbSNP
- rs3744983
- Type
- single nucleotide variant
- Location
- chr18:8380421 (GRCh38)
- Gene constraint
- LOEUF 0.334 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.38 · 5 PDB
- Residue 1304
- the tyrosine-protein phosphatase 2 domain
Disease context
PTPRM-related disorder
Similar variants
- 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
- PTPRM p.Asn439= 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-pro1304 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown