CERKL p.Val304=
c.912C>T · rs139270710 · VCV1652992
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -5.6 | GERP -3.2 |
| Overall | ||
| CADD | 0.086 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000434%
7/1,613,734 alleles · ultra-rare
exomes 5/1,461,544 · genomes 2/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| African / African-American | 0.00267% | 37,459 |
| European (non-Finnish) | 0.000339% | 294,970 |
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.Val304=
- Coding
- c.912C>T
- MANE Select
- NM_201548
- dbSNP
- rs139270710
- Type
- single nucleotide variant
- Location
- chr2:181548841 (GRCh38)
- Gene constraint
- LOEUF 1.43 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.82
- Residue 304
- the dagkc domain
Similar variants
- CERKL p.Val304Ala Uncertain significance ★ same residue
- 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
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-val304 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown