CEP85L p.Ser293=
c.879C>T · rs145696727 · VCV2656887
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0822%, 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 -0.14 | GERP -4.9, phastCons 0.002 |
| Overall | ||
| CADD | 11.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0822%
Middle Eastern · 5/6,084 alleles
Filtering AF
0.0633%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0618%
Overall
0.0545%
880/1,614,034 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0822% | 1,217 |
| European (non-Finnish) | 0.0672% | 1,488 |
| Remaining individualsnot grpmax-eligible | 0.0512% | 1,952 |
| Admixed American | 0.0367% | 2,728 |
| Finnishnot grpmax-eligible | 0.0266% | 3,766 |
| African / African-American | 0.00935% | 10,701 |
| South Asian | 0.00329% | 30,365 |
| East Asian | 0.00223% | 44,888 |
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
- CEP85L
- Protein
- p.Ser293=
- Coding
- c.879C>T
- MANE Select
- NM_001042475
- dbSNP
- rs145696727
- Type
- single nucleotide variant
- Location
- chr6:118565670 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.98
Similar variants
- PLN p.Arg9Cys Pathogenic ★★ ⚠ same type
- PLN p.Leu39Ter Pathogenic/Likely pathogenic ★★ same type
- CEP85L p.Arg151Gln Uncertain significance ★★ ⚠ same type
- CEP85L p.Arg241Ser Uncertain significance ★★ ⚠ same type
- CEP85L p.Gly122Ser Uncertain significance ★★ ⚠ same type
- CEP85L p.Ile186Val Uncertain significance ★★ ⚠ same type
- CEP85L p.Ile508Val Uncertain significance ★★ ⚠ same type
- CEP85L p.Pro152Ala Uncertain significance ★★ ⚠ 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/cep85l-p-ser293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown