CEP152 p.Pro1638=
c.4914A>G · rs150910683 · VCV158269
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.53%, afr)
Conditions
2
Seckel syndrome 5
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 -0.42 | GERP -0.76, phastCons 0.002 |
| Overall | ||
| CADD | 3.765 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.53%
African / African-American · 1,148/75,066 alleles
Filtering AF
1.46%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.43%
Overall
0.0791%
1,277/1,614,240 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.53% | 65 |
| Admixed American | 0.105% | 953 |
| Remaining individualsnot grpmax-eligible | 0.088% | 1,137 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.00329% | 30,363 |
| European (non-Finnish) | 0.000593% | 168,577 |
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.Pro1638=
- Coding
- c.4914A>G
- MANE Select
- NM_001194998
- dbSNP
- rs150910683
- Type
- single nucleotide variant
- Location
- chr15:48738468 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.54 · 3 PDB
Similar variants
- CEP152 c.1908+1G>T Likely pathogenic ★★ same condition
- CEP152 c.540+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CEP152 c.972+2T>A Likely pathogenic ★★ same condition
- CEP152 p.Arg115Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP152 p.Arg1309Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP152 p.Arg267Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP152 p.Arg987Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP152 p.Gln265Pro Pathogenic/Likely pathogenic ★★ same condition
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-pro1638 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown