CEP104 p.Thr628=
c.1884G>A · rs12144567 · VCV3031342
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0242%, sas)
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 -7.1 | GERP -3.7 |
| Overall | ||
| CADD | 0.737 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0242%
South Asian · 22/91,076 alleles
Filtering AF
0.0163%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0138%
Overall
0.00242%
39/1,614,154 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0242% | 4,140 |
| African / African-American | 0.00267% | 37,523 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,504 |
| European (non-Finnish) | 0.00119% | 84,288 |
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.Thr628=
- Coding
- c.1884G>A
- MANE Select
- NM_014704
- dbSNP
- rs12144567
- Type
- single nucleotide variant
- Location
- chr1:3829950 (GRCh38)
- Gene constraint
- LOEUF 0.851 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.75 · 2 PDB
- Residue 628
- a UniProt-annotated variant site (in mrt77); an α-helix
Similar variants
- CEP104 p.Thr628Met Conflicting classifications of pathogenicity ★ ⚠ same residue
- CEP104 c.2364+1G>A Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Arg299Ter Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Arg55Ter Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Arg631Ter Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Glu627Ter Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Lys270Ter Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Tyr253Ter 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/cep104-p-thr628 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown