CEP89 p.Arg102=
c.306G>A · rs10411735 · VCV1571867
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 54.7%, amr) — too common for a highly-penetrant pathogenic allele
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 0.24 | GERP -3.1, phastCons 0.99 |
| Overall | ||
| CADD | 3.542 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
54.7%
Admixed American · 32,792/59,898 alleles
Filtering AF
54.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 54%
Overall
34.4%
553,446/1,606,874 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 54.7% | 2 |
| East Asian | 43.4% | 2 |
| Amishnot grpmax-eligible | 41.5% | 2 |
| African / African-American | 38.1% | 3 |
| Finnishnot grpmax-eligible | 37.5% | 3 |
| South Asian | 35.4% | 3 |
| Remaining individualsnot grpmax-eligible | 33.6% | 3 |
| Middle Eastern | 33.6% | 3 |
| European (non-Finnish) | 32.7% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 32.1% | 3 |
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.Arg102=
- Coding
- c.306G>A
- MANE Select
- NM_032816
- dbSNP
- rs10411735
- Type
- single nucleotide variant
- Location
- chr19:32953801 (GRCh38)
- Gene constraint
- LOEUF 1.173 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.08
- Residue 102
- the 'disordered' region
Similar variants
- CEP89 p.Arg102Trp Uncertain significance ★★ ⚠ same residue
- CEP89 p.Arg102Gln Benign ★★ same residue
- 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
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-arg102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown