CEP152 p.Pro1243=
c.3729A>G · rs562708873 · VCV1663332
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.408%, 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 0.91 | GERP 0.49, phastCons 1 |
| Overall | ||
| CADD | 8.852 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.408%
South Asian · 366/89,752 alleles
Filtering AF
0.373%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.36%
Overall
0.0267%
429/1,608,702 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.408% | 245 |
| Middle Eastern | 0.0812% | 1,231 |
| Remaining individualsnot grpmax-eligible | 0.0193% | 5,186 |
| European (non-Finnish) | 0.0039% | 25,613 |
| East Asian | 0.00224% | 44,676 |
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.Pro1243=
- Coding
- c.3729A>G
- MANE Select
- NM_001194998
- dbSNP
- rs562708873
- Type
- single nucleotide variant
- Location
- chr15:48744898 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.54 · 3 PDB
Similar variants
- CEP152 p.Pro1243Ala 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
- CEP152 p.Arg1309Ter 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-pro1243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown