CEP78 p.Ile2=
c.6C>A · VCV3694156
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00135%, afr)
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 -0.067 | GERP -0.53, phastCons 0.67 |
| Overall | ||
| CADD | 12.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00135%
African / African-American · 1/74,252 alleles
Overall
7.03e-05%
1/1,422,260 alleles · very rare
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.Ile2=
- Coding
- c.6C>A
- MANE Select
- NM_001330691
- Type
- single nucleotide variant
- Location
- chr9:78236356 (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-ile2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown