CEP135 p.Arg908=
c.2724A>G · rs113687114 · VCV128697
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.36%, 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 -2.2 | GERP -3.5 |
| Overall | ||
| CADD | 0.745 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.36%
African / African-American · 2,506/74,530 alleles
Filtering AF
3.25%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.21%
Overall
0.188%
3,015/1,605,104 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.36% | 30 |
| Remaining individualsnot grpmax-eligible | 0.311% | 321 |
| Middle Eastern | 0.299% | 334 |
| Admixed American | 0.196% | 510 |
| Ashkenazi Jewishnot grpmax-eligible | 0.15% | 668 |
| European (non-Finnish) | 0.0115% | 8,709 |
| South Asian | 0.00445% | 22,451 |
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.Arg908=
- Coding
- c.2724A>G
- MANE Select
- NM_025009
- dbSNP
- rs113687114
- Type
- single nucleotide variant
- Location
- chr4:56011907 (GRCh38)
- Gene constraint
- LOEUF 0.989 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.15 · 2 PDB
Similar variants
- CEP135 p.Arg908Ter Pathogenic ★★ same residue
- CEP135 p.Arg908Gln Uncertain significance ★ ⚠ same residue
- 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.Leu578Ter 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-arg908 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown