PTPRQ p.Phe2181=
c.6543T>C · VCV4538033
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00548%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.074 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.18 | GERP -1.1, phastCons 0.99 |
| Overall | ||
| CADD | 7.704 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00548%
African / African-American · 4/72,980 alleles
Filtering AF
0.00178%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00106%
Overall
0.000258%
4/1,551,172 alleles · very rare
exomes 1/1,399,076 · genomes 3/152,096 · joint denominator
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.Phe2181=
- Coding
- c.6543T>C
- MANE Select
- NM_001145026
- Type
- single nucleotide variant
- Location
- chr12:80670433 (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 2181
- the tyrosine-protein phosphatase domain; a β-strand
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-phe2181 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown