STK36 p.Pro169=
c.507A>G · VCV4959827
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.34 | GERP -0.56, phastCons 0.47 |
| Overall | ||
| CADD | 9.525 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,012 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000434%
7/1,614,186 alleles · very rare
exomes 7/1,461,890 · genomes 0/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,012 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
| European (non-Finnish) | 0.000424% | 236,008 |
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
- STK36
- Protein
- p.Pro169=
- Coding
- c.507A>G
- MANE Select
- NM_015690
- Type
- single nucleotide variant
- Location
- chr2:218676101 (GRCh38)
- Gene constraint
- LOEUF 0.912 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.22
- Residue 169
- the protein kinase domain
Similar variants
- STK36 p.Ala1215Thr Uncertain significance ★★ ⚠ same type
- STK36 p.Arg1209Trp Uncertain significance ★★ same type
- STK36 p.Arg218Cys Uncertain significance ★★ ⚠ same type
- STK36 p.Arg56Trp Uncertain significance ★★ ⚠ same type
- STK36 p.Arg59Trp Uncertain significance ★★ ⚠ same type
- STK36 p.Leu1081Pro Uncertain significance ★★ ⚠ same type
- STK36 p.Leu122Pro Uncertain significance ★★ ⚠ same type
- STK36 p.Lys161Arg Uncertain significance ★★ 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/stk36-p-pro169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown