CEP152 p.Phe1671fs
c.5012del · rs1892713617 · VCV2813331
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (27 of 27) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 0.69, phastCons 0.26 |
| Overall | ||
| CADD | 23.9 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
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.Phe1671fs
- Coding
- c.5012del
- MANE Select
- NM_001194998
- dbSNP
- rs1892713617
- Type
- Deletion
- Location
- chr15:48738370 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.54 · 3 PDB
Similar variants
- CEP152 p.Gln1058fs Pathogenic/Likely pathogenic ★★ same type
- CEP152 p.Leu1071fs Pathogenic/Likely pathogenic ★★ same type
- CEP152 p.Lys764fs Likely pathogenic ★★ same type
- CEP152 p.Phe225_Leu226insTer Pathogenic/Likely pathogenic ★★ same type
- CEP152 p.Thr1006fs Pathogenic/Likely pathogenic ★★ same type
- CEP152 p.Thr386fs Pathogenic ★★ same type
- CEP152 p.Tyr678_Gln679delinsTer Pathogenic ★★ same type
- CEP152 p.Val1084fs 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-phe1671fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown