CEP85L p.Ser157=
c.471A>G · VCV4681468
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, 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 -0.81 | GERP -1.1, phastCons 0.017 |
| Overall | ||
| CADD | 6.899 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,062 alleles
Filtering AF
0.00582%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00242%
Overall
0.00041%
6/1,461,888 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
| South Asian | 0.0011% | 91,084 |
| European (non-Finnish) | 0.000169% | 590,023 |
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.Ser157=
- Coding
- c.471A>G
- MANE Select
- NM_001042475
- Type
- single nucleotide variant
- Location
- chr6:118566078 (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-ser157 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown