CEP85L p.Arg465=
c.1395A>G · rs2533916236 · VCV2656884
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
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 1.9 | phastCons 0.89 |
| Overall | ||
| CADD | 9.362 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,604 alleles
Overall
6.85e-05%
1/1,460,902 alleles · very rare
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.Arg465=
- Coding
- c.1395A>G
- MANE Select
- NM_001042475
- dbSNP
- rs2533916236
- Type
- single nucleotide variant
- Location
- chr6:118491728 (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-arg465 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown