PTPRQ p.Ser481=
c.1443G>A · rs373744641 · VCV1197806
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.444%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.021 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.014 | GERP -3.8, phastCons 0.92 |
| Overall | ||
| CADD | 2.898 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.444%
South Asian · 373/83,964 alleles
Filtering AF
0.407%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.392%
Overall
0.0477%
740/1,550,014 alleles · rare
exomes 601/1,397,962 · genomes 139/152,052 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.444% | 225 |
| Middle Eastern | 0.318% | 315 |
| African / African-American | 0.204% | 490 |
| Remaining individualsnot grpmax-eligible | 0.0616% | 1,622 |
| East Asian | 0.0196% | 5,108 |
| Admixed American | 0.0157% | 6,364 |
| European (non-Finnish) | 0.0127% | 7,849 |
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
- PTPRQ
- Protein
- p.Ser481=
- Coding
- c.1443G>A
- MANE Select
- NM_001145026
- dbSNP
- rs373744641
- Type
- single nucleotide variant
- Location
- chr12:80493358 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 75.35 · 1 PDB
- Residue 481
- the fibronectin type-iii 5 domain
Similar variants
- PTPRQ c.1359+2T>C Pathogenic/Likely pathogenic ★★ same type
- PTPRQ c.6024+2T>C Pathogenic ★★ same type
- PTPRQ c.6025-1G>A Pathogenic/Likely pathogenic ★★ same type
- PTPRQ c.6327+1G>A Likely pathogenic ★★ same type
- PTPRQ p.Arg1747Ter Pathogenic/Likely pathogenic ★★ same type
- PTPRQ p.Arg2159Ter Pathogenic ★★ same type
- PTPRQ p.Gln1336Ter Pathogenic ★★ same type
- PTPRQ p.Ser874Ter Likely pathogenic ★★ 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/ptprq-p-ser481 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown