CEP78 p.Arg693=
c.2077A>C · rs61730339 · VCV667042
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.766%, 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 8 | GERP 0.71, phastCons 1 |
| Overall | ||
| CADD | 10.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.766%
African / African-American · 575/75,026 alleles
Filtering AF
0.715%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.694%
Overall
0.0492%
793/1,612,238 alleles · rare
exomes 457/1,459,932 · genomes 336/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.766% | 130 |
| Remaining individualsnot grpmax-eligible | 0.107% | 932 |
| Admixed American | 0.0988% | 1,012 |
| Middle Eastern | 0.0825% | 1,212 |
| European (non-Finnish) | 0.00729% | 13,710 |
| South Asian | 0.0011% | 90,654 |
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.Arg693=
- Coding
- c.2077A>C
- MANE Select
- NM_001330691
- dbSNP
- rs61730339
- Type
- single nucleotide variant
- Location
- chr9:78266673 (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-arg693 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown