PTK2 p.Ile528=
c.1584T>A · rs974857571 · VCV751734
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.15 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.36 | acceptor loss · deltas |
| Pangolin | Δ0.22 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -3.7 | GERP -3.7 |
| Overall | ||
| CADD | 0.199 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PTK2
- Protein
- p.Ile528=
- Coding
- c.1584T>A
- MANE Select
- NM_001352702
- dbSNP
- rs974857571
- Type
- single nucleotide variant
- Location
- chr8:140746817 (GRCh38)
- Gene constraint
- LOEUF 0.399 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.10 · 40 PDB
- Residue 528
- an α-helix; the protein kinase domain
Similar variants
- PTK2 p.Arg855Ter Uncertain significance ★★ same type
- PTK2 c.*705T>A Benign ★★ same type
- PTK2 p.Arg349= Benign ★★ same type
- PTK2 p.Asp703= Benign ★★ same type
- PTK2 p.Glu870= Benign/Likely benign ★★ same type
- PTK2 p.Pro690= Benign ★★ same type
- PTK2 p.Ser355= Benign ★★ same type
- PTK2 p.Tyr969= 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/ptk2-p-ile528 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown