PTPRQ p.Phe1925fs
c.5775del · VCV3393554
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 34 of 45 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP -3, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PTPRQ
- Protein
- p.Phe1925fs
- Coding
- c.5775del
- MANE Select
- NM_001145026
- Type
- Deletion
- Location
- chr12:80632276 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 75.35 · 1 PDB
Similar variants
- PTPRQ p.Ala1069fs Likely pathogenic ★★ same type
- PTPRQ p.Thr558fs Pathogenic ★★ same type
- PTPRQ c.1186+18del Likely benign ★★ same type
- PTPRQ p.Thr51_Thr54del Benign/Likely benign ★★ same type
- PTPRQ p.Ala1398fs Likely pathogenic ★ same type
- PTPRQ p.Gln1678fs Likely pathogenic ★ same type
- PTPRQ p.Glu909fs Pathogenic ★ same type
- PTPRQ p.Leu1103fs 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-phe1925fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown