CEP135 p.Pro179=
c.537C>G · rs769365357 · VCV3052747
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.01%, amr)
Conditions
1
CEP135-related disorder
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 -0.71 | GERP -1.2, phastCons 0.006 |
| Overall | ||
| CADD | 8.405 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/59,992 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.000558%
9/1,614,002 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 9,999 |
| European (non-Finnish) | 0.000254% | 393,332 |
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
- CEP135
- Protein
- p.Pro179=
- Coding
- c.537C>G
- MANE Select
- NM_025009
- dbSNP
- rs769365357
- Type
- single nucleotide variant
- Location
- chr4:55957287 (GRCh38)
- Gene constraint
- LOEUF 0.989 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.15 · 2 PDB
Disease context
CEP135-related disorder
Similar variants
- CEP135 p.Arg686Ter Likely pathogenic ★ same condition
- CEP135 p.Thr114Ile Uncertain significance ⚠ same condition
- CEP135 c.1780-7T>C Likely benign same condition
- CEP135 c.473-7T>C Likely benign same condition
- CEP135 p.His1048fs Pathogenic/Likely pathogenic ★★ same condition
- CEP135 p.Asp682fs Likely pathogenic ★ same condition
- CEP135 c.473-1G>C Likely pathogenic ★★ same type
- CEP135 p.Arg1083Ter Pathogenic/Likely pathogenic ★★ 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/cep135-p-pro179 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown