CEP104 p.Pro361=
c.1083G>A · rs61740614 · VCV1286187
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.61%, afr)
Conditions
1
Joubert syndrome 25
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 -0.69 | GERP -0.42 |
| Overall | ||
| CADD | 7.597 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.61%
African / African-American · 1,209/74,988 alleles
Filtering AF
1.54%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.51%
Overall
0.0943%
1,521/1,613,762 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.61% | 62 |
| Admixed American | 0.095% | 1,053 |
| Remaining individualsnot grpmax-eligible | 0.0928% | 1,078 |
| European (non-Finnish) | 0.016% | 6,242 |
| South Asian | 0.00659% | 15,176 |
| East Asian | 0.00223% | 44,878 |
| Finnishnot grpmax-eligible | 0.00156% | 64,010 |
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
- CEP104
- Protein
- p.Pro361=
- Coding
- c.1083G>A
- MANE Select
- NM_014704
- dbSNP
- rs61740614
- Type
- single nucleotide variant
- Location
- chr1:3837328 (GRCh38)
- Gene constraint
- LOEUF 0.851 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.75 · 2 PDB
- Residue 361
- a UniProt-annotated variant site (in mrt77)
Similar variants
- CEP104 p.Pro361Arg Uncertain significance ★★ ⚠ same residue
- CEP104 p.Pro361fs Pathogenic ★ same residue
- CEP104 p.Pro361Leu Uncertain significance ★★ ⚠ same residue
- CEP104 p.Pro361Ala Uncertain significance ★ ⚠ same residue
- CEP104 p.Arg299Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP104 p.Arg55Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP104 p.Glu627Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP104 p.Lys270Ter Pathogenic/Likely pathogenic ★★ 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/cep104-p-pro361 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown