STK36 p.Asp488=
c.1464T>C · rs73079060 · VCV1221626
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 21.2%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.5 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 8.589 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
21.2%
African / African-American · 15,886/75,010 alleles
Filtering AF
20.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 20.8%
Overall
1.13%
18,267/1,614,122 alleles · common
exomes 9,071/1,461,804 · genomes 9,196/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 21.2% | 5 |
| Remaining individualsnot grpmax-eligible | 1.54% | 65 |
| Admixed American | 1.42% | 71 |
| Middle Eastern | 0.794% | 126 |
| South Asian | 0.0758% | 1,320 |
| European (non-Finnish) | 0.038% | 2,628 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,802 |
| East Asian | 0.00223% | 44,882 |
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.Asp488=
- Coding
- c.1464T>C
- MANE Select
- NM_015690
- dbSNP
- rs73079060
- Type
- single nucleotide variant
- Location
- chr2:218688780 (GRCh38)
- Gene constraint
- LOEUF 0.912 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.22
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-asp488 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown