CERKL p.Arg9=
c.27G>C · rs368855330 · VCV1087156
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00684%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.57 | donor loss at this position · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -1.6 |
| Overall | ||
| CADD | 13.82 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00684%
East Asian · 3/43,842 alleles
Filtering AF
0.00181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000903%
Overall
0.00028%
4/1,429,370 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00684% | 14,614 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 61,056 |
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.Arg9=
- Coding
- c.27G>C
- MANE Select
- NM_201548
- dbSNP
- rs368855330
- Type
- single nucleotide variant
- Location
- chr2:181656980 (GRCh38)
- Gene constraint
- LOEUF 1.43 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.82
- Residue 9
- 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-arg9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown