Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 13 submitters
gnomAD v4.1
Common
common (popmax 78.3%, sas) — too common for a highly-penetrant pathogenic allele
Conditions
3
inherited retinal dystrophy
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 1.5 | GERP -3.4, phastCons 1 |
| Overall | ||
| CADD | 10.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
78.3%
South Asian · 70,683/90,324 alleles
Filtering AF
77.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 77.6%
Overall
49.1%
786,057/1,601,126 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 78.3% | 1 |
| East Asian | 72.8% | 1 |
| Admixed American | 58.2% | 2 |
| Middle Eastern | 56.2% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 54.1% | 2 |
| Remaining individualsnot grpmax-eligible | 50.2% | 2 |
| European (non-Finnish) | 47.5% | 2 |
| Finnishnot grpmax-eligible | 39.6% | 3 |
| African / African-American | 22.4% | 4 |
| Amishnot grpmax-eligible | 21.6% | 5 |
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.Phe52=
- Coding
- c.156C>T
- MANE Select
- NM_201548
- dbSNP
- rs1473295
- Type
- single nucleotide variant
- Location
- chr2:181656851 (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 condition
- CERKL c.1074-2A>C Likely pathogenic ★★ same condition
- CERKL c.1074-2A>G Likely pathogenic ★★ same condition
- CERKL c.1365+1G>A Likely pathogenic ★★ same condition
- CERKL c.1366-1G>A Likely pathogenic ★★ same condition
- CERKL c.1366-1G>T Likely pathogenic ★★ same condition
- CERKL c.1366-2A>G Likely pathogenic ★★ same condition
- CERKL c.238+1G>A Pathogenic ★★ same condition
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-phe52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown