CEP85 p.Ala53=
c.159C>A · rs115133994 · VCV736564
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.546%, afr)
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 -0.98 | GERP -3.4, phastCons 0.005 |
| Overall | ||
| CADD | 6.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.546%
African / African-American · 409/74,930 alleles
Filtering AF
0.502%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.485%
Overall
0.0332%
535/1,613,762 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.546% | 183 |
| Admixed American | 0.0617% | 1,621 |
| Remaining individualsnot grpmax-eligible | 0.0416% | 2,403 |
| European (non-Finnish) | 0.00534% | 18,729 |
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
- CEP85
- Protein
- p.Ala53=
- Coding
- c.159C>A
- MANE Select
- NM_001319944
- dbSNP
- rs115133994
- Type
- single nucleotide variant
- Location
- chr1:26244269 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.09 · 2 PDB
Similar variants
- CEP85 p.Ala176= Benign ★★ same type
- CEP85 p.Leu405Phe Benign ★★ same type
- CEP85 p.Ala374Pro Uncertain significance ★ ⚠ same type
- CEP85 p.Ala396Thr Uncertain significance ★ ⚠ same type
- CEP85 p.Ala399Ser Uncertain significance ★ ⚠ same type
- CEP85 p.Ala656Val Uncertain significance ★ ⚠ same type
- CEP85 p.Arg146Lys Uncertain significance ★ ⚠ same type
- CEP85 p.Arg177Lys 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/cep85-p-ala53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown