CEP89 p.Gln443=
c.1329G>A · rs115250365 · VCV1636204
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.572%, 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 0.53 | GERP -0.32, phastCons 0.072 |
| Overall | ||
| CADD | 4.548 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.572%
African / African-American · 429/75,064 alleles
Filtering AF
0.527%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.509%
Overall
0.0321%
518/1,614,212 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.572% | 175 |
| Middle Eastern | 0.115% | 866 |
| Remaining individualsnot grpmax-eligible | 0.0704% | 1,421 |
| Admixed American | 0.0483% | 2,070 |
| South Asian | 0.00769% | 13,012 |
| European (non-Finnish) | 0.000169% | 590,019 |
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
- CEP89
- Protein
- p.Gln443=
- Coding
- c.1329G>A
- MANE Select
- NM_032816
- dbSNP
- rs115250365
- Type
- single nucleotide variant
- Location
- chr19:32918279 (GRCh38)
- Gene constraint
- LOEUF 1.173 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.08
Similar variants
- CEP89 p.Ala291Thr Uncertain significance ★★ ⚠ same type
- CEP89 p.Ala291Val Uncertain significance ★★ ⚠ same type
- CEP89 p.Ala372Thr Uncertain significance ★★ ⚠ same type
- CEP89 p.Ala54Val Uncertain significance ★★ ⚠ same type
- CEP89 p.Ala680Thr Uncertain significance ★★ ⚠ same type
- CEP89 p.Ala780Asp Uncertain significance ★★ ⚠ same type
- CEP89 p.Arg102Trp Uncertain significance ★★ ⚠ same type
- CEP89 p.Arg324Cys Uncertain significance ★★ ⚠ 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/cep89-p-gln443 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown