CERKL p.Pro23=
c.69G>A · rs200432563 · VCV1167593
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.104%, eas)
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 0.04 | GERP 0.48 |
| Overall | ||
| CADD | 7.919 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.104%
East Asian · 46/44,074 alleles
Filtering AF
0.0803%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0719%
Overall
0.00315%
50/1,589,176 alleles · rare
exomes 43/1,436,858 · genomes 7/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.104% | 958 |
| Middle Eastern | 0.0201% | 4,966 |
| European (non-Finnish) | 0.000257% | 388,933 |
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
- CERKL
- Protein
- p.Pro23=
- Coding
- c.69G>A
- MANE Select
- NM_201548
- dbSNP
- rs200432563
- Type
- single nucleotide variant
- Location
- chr2:181656938 (GRCh38)
- Gene constraint
- LOEUF 1.43 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.82
- Residue 23
- the 'disordered' region
Similar variants
- CERKL c.1074-1G>C Pathogenic/Likely pathogenic ★★ same type
- CERKL c.1074-2A>C Likely pathogenic ★★ same type
- CERKL c.1074-2A>G Likely pathogenic ★★ same type
- CERKL c.1365+1G>A Likely pathogenic ★★ same type
- CERKL c.1366-1G>A Likely pathogenic ★★ same type
- CERKL c.1366-1G>T Likely pathogenic ★★ same type
- CERKL c.1366-2A>G Likely pathogenic ★★ same type
- CERKL c.238+1G>A Pathogenic ★★ 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/cerkl-p-pro23 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown