CEP152 p.Ala1153=
c.3459A>G · rs774053933 · VCV2978459
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, sas)
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 -0.64 | GERP 1.9, phastCons 0.029 |
| Overall | ||
| CADD | 2.596 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
South Asian · 15/91,072 alleles
Filtering AF
0.0101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00811%
Overall
0.00109%
16/1,461,776 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0165% | 6,071 |
| European (non-Finnish) | 8.47e-05% | 1,180,006 |
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.Ala1153=
- Coding
- c.3459A>G
- MANE Select
- NM_001194998
- dbSNP
- rs774053933
- Type
- single nucleotide variant
- Location
- chr15:48752356 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.54 · 3 PDB
Similar variants
- 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
- CEP152 p.Arg1309Ter Pathogenic/Likely pathogenic ★★ same type
- CEP152 p.Arg267Ter 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-ala1153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown