CEP104 p.Pro846=
c.2538C>T · rs1209375429 · VCV3030927
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
Conditions
1
CEP104-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.072 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.5 | GERP -4 |
| Overall | ||
| CADD | 1.288 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,898 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000248%
4/1,614,088 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,966 |
| European (non-Finnish) | 8.47e-05% | 1,180,050 |
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.Pro846=
- Coding
- c.2538C>T
- MANE Select
- NM_014704
- dbSNP
- rs1209375429
- Type
- single nucleotide variant
- Location
- chr1:3823207 (GRCh38)
- Gene constraint
- LOEUF 0.851 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.75 · 2 PDB
- Residue 846
- a UniProt-annotated variant site (in mrt77); a turn
Disease context
CEP104-related disorder
Similar variants
- CEP104 p.Pro846Leu Uncertain significance ★ ⚠ same residue
- CEP104 c.2364+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CEP104 p.Arg55Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP104 p.Arg166Ter Likely pathogenic ★ same condition
- CEP104 p.Glu296Ter Likely pathogenic ★ same condition
- CEP104 p.Glu45Ter Likely pathogenic ★ same condition
- CEP104 p.Glu521Ter Likely pathogenic ★ same condition
- CEP104 c.736-2A>T Conflicting classifications of pathogenicity ★ 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-pro846 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown