CERK p.Pro509=
c.1527T>A · rs34110809 · VCV777761
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.52%, afr)
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 -13 | GERP -3 |
| Overall | ||
| CADD | 0.021 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.52%
African / African-American · 3,384/74,902 alleles
Filtering AF
4.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.34%
Overall
0.249%
3,995/1,607,210 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.52% | 22 |
| Remaining individualsnot grpmax-eligible | 0.354% | 282 |
| Middle Eastern | 0.314% | 318 |
| Admixed American | 0.301% | 332 |
| European (non-Finnish) | 0.0152% | 6,590 |
| South Asian | 0.0121% | 8,261 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00339% | 29,504 |
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
- CERK
- Protein
- p.Pro509=
- Coding
- c.1527T>A
- MANE Select
- NM_022766
- dbSNP
- rs34110809
- Type
- single nucleotide variant
- Location
- chr22:46690006 (GRCh38)
- Gene constraint
- LOEUF 0.829 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.86
Similar variants
- CERK p.His113= Benign ★★ same type
- CERK p.Thr461Met Benign ★★ same type
- CERK p.Ala215Thr Uncertain significance ★ ⚠ same type
- CERK p.Ala215Val Uncertain significance ★ ⚠ same type
- CERK p.Ala238Ser Uncertain significance ★ ⚠ same type
- CERK p.Ala238Thr Uncertain significance ★ ⚠ same type
- CERK p.Ala254Thr Uncertain significance ★ ⚠ same type
- CERK p.Ala258Val 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/cerk-p-pro509 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown