CEP78 p.Pro391=
c.1173G>A · rs540373914 · VCV1145275
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.029%, 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 -12 | GERP -2.8 |
| Overall | ||
| CADD | 1.831 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.029%
East Asian · 13/44,838 alleles
Filtering AF
0.0171%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.00637%
102/1,601,274 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.029% | 3,449 |
| European (non-Finnish) | 0.00709% | 14,107 |
| Remaining individualsnot grpmax-eligible | 0.00486% | 20,566 |
| South Asian | 0.00223% | 44,777 |
| African / African-American | 0.00133% | 74,948 |
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.Pro391=
- Coding
- c.1173G>A
- MANE Select
- NM_001330691
- dbSNP
- rs540373914
- Type
- single nucleotide variant
- Location
- chr9:78252011 (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 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
- CEP78 p.Arg483Ter Pathogenic/Likely pathogenic ★★ same type
- CEP78 p.Cys158Phe 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/cep78-p-pro391 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown