PTPRJ p.Asp94=
c.282T>C · rs142849806 · VCV2641771
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.21%, nfe)
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 -3.8 | GERP -2.7 |
| Overall | ||
| CADD | 0.162 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.21%
European (non-Finnish) · 2,480/1,180,030 alleles
Filtering AF
0.203%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.2%
Overall
0.172%
2,773/1,614,152 alleles · rare
exomes 2,632/1,461,880 · genomes 141/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.21% | 476 |
| Remaining individualsnot grpmax-eligible | 0.13% | 772 |
| South Asian | 0.109% | 920 |
| Finnishnot grpmax-eligible | 0.089% | 1,123 |
| Admixed American | 0.055% | 1,819 |
| African / African-American | 0.0293% | 3,411 |
| East Asian | 0.00223% | 44,882 |
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
- PTPRJ
- Protein
- p.Asp94=
- Coding
- c.282T>C
- MANE Select
- NM_002843
- dbSNP
- rs142849806
- Type
- single nucleotide variant
- Location
- chr11:48112913 (GRCh38)
- Gene constraint
- LOEUF 1.043 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.58 · 5 PDB
- Residue 94
- the 'disordered' region
Similar variants
- PTPRJ p.Asp94Asn Uncertain significance ★ ⚠ same residue
- PTPRJ p.Gln356Arg Uncertain significance ★★ ⚠ same type
- PTPRJ p.Gly773Asp Uncertain significance ★★ ⚠ same type
- PTPRJ c.3042-6A>G Benign ★★ same type
- PTPRJ p.Ala293Thr Benign ★★ same type
- PTPRJ p.Arg418His Likely benign ★★ same type
- PTPRJ p.Asn192Ser Benign ★★ same type
- PTPRJ p.His451Arg Benign ★★ 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/ptprj-p-asp94 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown