CEP152 p.Arg1309=
c.3927A>G · rs1414687397 · VCV2802628
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.84e-05%)
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 -2.4 | GERP -3.5 |
| Overall | ||
| CADD | 5.874 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.84e-05%
Overall
6.84e-05%
1/1,461,870 alleles · very rare
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
- CEP152
- Protein
- p.Arg1309=
- Coding
- c.3927A>G
- MANE Select
- NM_001194998
- dbSNP
- rs1414687397
- Type
- single nucleotide variant
- Location
- chr15:48742009 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.54 · 3 PDB
- Residue 1309
- an α-helix
Similar variants
- CEP152 p.Arg1309Ter Pathogenic/Likely pathogenic ★★ same residue
- CEP152 p.Arg1309Gln Uncertain significance ★ ⚠ same residue
- CEP152 c.1578-1G>A Likely pathogenic ★★ same type
- CEP152 c.1908+1G>T Likely pathogenic ★★ same type
- CEP152 c.540+1G>A Pathogenic/Likely pathogenic ★★ same type
- CEP152 c.88-2A>G Likely pathogenic ★★ same type
- CEP152 c.972+2T>A Likely pathogenic ★★ same type
- CEP152 p.Arg115Ter 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/cep152-p-arg1309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown