CEP78 p.Phe15=
c.45C>T · rs748284703 · VCV1113978
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00227%, eas)
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 -0.13 | GERP -1.4, phastCons 0.14 |
| Overall | ||
| CADD | 12.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00227%
East Asian · 1/43,968 alleles
Filtering AF
0.00154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00131%
Overall
0.00169%
27/1,594,820 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00227% | 43,968 |
| European (non-Finnish) | 0.00222% | 45,077 |
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
- CEP78
- Protein
- p.Phe15=
- Coding
- c.45C>T
- MANE Select
- NM_001330691
- dbSNP
- rs748284703
- Type
- single nucleotide variant
- Location
- chr9:78236395 (GRCh38)
- Gene constraint
- LOEUF 1.531 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.28
Similar variants
- CEP78 p.Phe15Leu Uncertain significance ★ ⚠ same residue
- CEP78 p.Phe15fs Likely pathogenic ★ same residue
- CEP78 c.1205+2T>A Pathogenic/Likely pathogenic ★★ same type
- CEP78 c.1206-2A>C Pathogenic ★★ same type
- CEP78 c.1206-2A>G Pathogenic/Likely pathogenic ★★ same type
- CEP78 c.1251+5G>A Pathogenic/Likely pathogenic ★★ same type
- CEP78 c.254-1G>T Pathogenic/Likely pathogenic ★★ same type
- CEP78 c.778+1G>A 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/cep78-p-phe15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown