CEP135 p.His99=
c.297C>T · rs115408010 · VCV128700
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.99%, 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 -1.2 | GERP -2.9 |
| Overall | ||
| CADD | 0.622 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.99%
African / African-American · 689/69,598 alleles
Filtering AF
0.929%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.904%
Overall
0.0865%
1,304/1,508,172 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.99% | 101 |
| Middle Eastern | 0.484% | 207 |
| Admixed American | 0.172% | 581 |
| Remaining individualsnot grpmax-eligible | 0.154% | 648 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0393% | 2,544 |
| European (non-Finnish) | 0.0369% | 2,711 |
| South Asian | 0.00522% | 19,164 |
| Finnishnot grpmax-eligible | 0.00163% | 61,440 |
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.His99=
- Coding
- c.297C>T
- MANE Select
- NM_025009
- dbSNP
- rs115408010
- Type
- single nucleotide variant
- Location
- chr4:55953268 (GRCh38)
- Gene constraint
- LOEUF 0.989 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.15 · 2 PDB
- Residue 99
- an α-helix
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-his99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown