CEP78 p.Arg39Pro
c.116G>C · rs779694885 · VCV1022448
Computational evidence
| Protein change | ||
| AlphaMissense | 0.3203 | likely benign |
|---|---|---|
| REVEL | 0.131 | moderately benign-leaning |
| SaProt | LLR -1.43 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 8.3 | GERP 1.6, phastCons 1 |
| Regional constraint | o/e 1.08 | unconstrained · MANE · 34 kb · p 0.014 · regional, not allelic |
| Overall | ||
| CADD | 23.6 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0496% | 2,015 |
| African / African-American | 0.00801% | 12,490 |
| Remaining individualsnot grpmax-eligible | 0.00483% | 20,713 |
| European (non-Finnish) | 0.00051% | 196,105 |
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.Arg39Pro
- Coding
- c.116G>C
- MANE Select
- NM_001330691
- dbSNP
- rs779694885
- Type
- single nucleotide variant
- Location
- chr9:78236466 (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.2107+37C>T Uncertain significance ★★ same condition
- CEP78 p.Ala304Thr Uncertain significance ★★ ⚠ same condition
- CEP78 p.Ala378Val Uncertain significance ★★ ⚠ same condition
- CEP78 p.Ala380Ser Uncertain significance ★★ ⚠ same condition
- CEP78 p.Ala380Thr Uncertain significance ★★ ⚠ same condition
- CEP78 p.Ala47Thr Uncertain significance ★★ ⚠ same condition
- CEP78 p.Ala56Val Uncertain significance ★★ ⚠ same condition
- CEP78 p.Ala579Val Uncertain significance ★★ ⚠ same condition
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-arg39pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown