PTK2 p.Pro690=
c.2070T>C · rs149694113 · VCV717392
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.04%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.446 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -3.7 |
| Overall | ||
| CADD | 4.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.04%
South Asian · 945/91,080 alleles
Filtering AF
0.983%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.961%
Overall
0.285%
4,593/1,614,138 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.04% | 96 |
| Ashkenazi Jewishnot grpmax-eligible | 0.696% | 144 |
| Middle Eastern | 0.577% | 173 |
| Remaining individualsnot grpmax-eligible | 0.267% | 374 |
| European (non-Finnish) | 0.262% | 382 |
| Finnishnot grpmax-eligible | 0.116% | 865 |
| Admixed American | 0.0616% | 1,622 |
| African / African-American | 0.048% | 2,085 |
| East Asian | 0.00446% | 22,435 |
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
- PTK2
- Protein
- p.Pro690=
- Coding
- c.2070T>C
- MANE Select
- NM_001352702
- dbSNP
- rs149694113
- Type
- single nucleotide variant
- Location
- chr8:140735334 (GRCh38)
- Gene constraint
- LOEUF 0.399 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.10 · 40 PDB
- Residue 690
- the 'disordered' region
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.Ser355= Benign ★★ same type
- PTK2 p.Tyr969= Benign ★★ same type
- PTK2 p.Val215= 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-pro690 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown