CEP104 p.Ser406=
c.1218C>T · VCV3702483
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
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 -2.1 | GERP -3.9 |
| Overall | ||
| CADD | 1.785 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,032 alleles
Filtering AF
0.000877%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000548%
8/1,459,184 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,032 |
| South Asian | 0.0033% | 30,303 |
| European (non-Finnish) | 0.00034% | 294,469 |
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.Ser406=
- Coding
- c.1218C>T
- MANE Select
- NM_014704
- Type
- single nucleotide variant
- Location
- chr1:3836594 (GRCh38)
- Gene constraint
- LOEUF 0.851 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.75 · 2 PDB
- Residue 406
- a UniProt-annotated variant site (in mrt77)
Similar variants
- CEP104 p.Ser406Asn Uncertain significance ★ ⚠ same residue
- CEP104 p.Ser406Gly 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
- CEP104 p.Tyr253Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP104 c.1120-5T>A 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/cep104-p-ser406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown