CEP152 p.Asp62=
c.186C>T · rs548567364 · VCV210685
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0496%, mid)
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 -0.46 | GERP 0.48 |
| Overall | ||
| CADD | 2.542 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0496%
Middle Eastern · 3/6,054 alleles
Filtering AF
0.0317%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0273%
Overall
0.013%
210/1,613,378 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0496% | 2,018 |
| Admixed American | 0.045% | 2,221 |
| European (non-Finnish) | 0.0136% | 7,372 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,808 |
| East Asian | 0.00668% | 14,959 |
| African / African-American | 0.00667% | 15,001 |
| South Asian | 0.00439% | 22,757 |
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.Asp62=
- Coding
- c.186C>T
- MANE Select
- NM_001194998
- dbSNP
- rs548567364
- Type
- single nucleotide variant
- Location
- chr15:48797953 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.54 · 3 PDB
- Residue 62
- the 'disordered' region
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-asp62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown