CEP89 p.Val753=
c.2259T>G · rs745959 · VCV1599009
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 36.5%, nfe) — 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 0.34 | GERP -0.79, phastCons 0.001 |
| Overall | ||
| CADD | 1.949 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
36.5%
European (non-Finnish) · 430,020/1,179,472 alleles
Filtering AF
36.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 36.3%
Overall
32.1%
518,445/1,613,506 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 36.5% | 3 |
| Amishnot grpmax-eligible | 30.6% | 3 |
| Finnishnot grpmax-eligible | 30.3% | 3 |
| Remaining individualsnot grpmax-eligible | 30.1% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 28.9% | 3 |
| Middle Eastern | 24.4% | 4 |
| South Asian | 21% | 5 |
| Admixed American | 15.4% | 6 |
| African / African-American | 9.77% | 10 |
| East Asian | 9.48% | 11 |
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.Val753=
- Coding
- c.2259T>G
- MANE Select
- NM_032816
- dbSNP
- rs745959
- Type
- single nucleotide variant
- Location
- chr19:32879255 (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-val753 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown