CEP135 p.Lys458=
c.1374G>A · rs999052618 · VCV2904288
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00576%, 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 4 | GERP 0.14, phastCons 1 |
| Overall | ||
| CADD | 10.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00576%
European (non-Finnish) · 68/1,179,868 alleles
Filtering AF
0.00462%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00423%
Overall
0.0044%
71/1,613,704 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00576% | 17,351 |
| African / African-American | 0.00267% | 37,450 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,462 |
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.Lys458=
- Coding
- c.1374G>A
- MANE Select
- NM_025009
- dbSNP
- rs999052618
- Type
- single nucleotide variant
- Location
- chr4:55974870 (GRCh38)
- Gene constraint
- LOEUF 0.989 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.15 · 2 PDB
Similar variants
- CEP135 c.473-1G>C Likely pathogenic ★★ same type
- CEP135 p.Arg1083Ter Pathogenic/Likely pathogenic ★★ same type
- CEP135 p.Arg292Ter Pathogenic/Likely pathogenic ★★ same type
- CEP135 p.Arg418Ter Pathogenic ★★ same type
- CEP135 p.Arg470Ter Pathogenic/Likely pathogenic ★★ same type
- CEP135 p.Arg908Ter Pathogenic ★★ same type
- CEP135 p.Leu578Ter Pathogenic ★★ same type
- CEP135 p.Lys1071Ter 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-lys458 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown