CERKL p.Ala79=
c.237G>T · rs374655559 · VCV1125908
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0646%, amr)
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 -2 | GERP -5 |
| Overall | ||
| CADD | 7.165 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0646%
Admixed American · 38/58,834 alleles
Filtering AF
0.0483%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0427%
Overall
0.00258%
41/1,590,668 alleles · ultra-rare
exomes 37/1,439,076 · genomes 4/151,592 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0646% | 1,548 |
| Remaining individualsnot grpmax-eligible | 0.00327% | 30,616 |
| European (non-Finnish) | 8.56e-05% | 1,168,126 |
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.Ala79=
- Coding
- c.237G>T
- MANE Select
- NM_201548
- dbSNP
- rs374655559
- Type
- single nucleotide variant
- Location
- chr2:181656770 (GRCh38)
- Gene constraint
- LOEUF 1.43 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.82
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-ala79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown