CEP89 p.Glu139=
c.417A>G · rs74954479 · VCV2068552
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.231%, 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 -0.65 | GERP -3.1 |
| Overall | ||
| CADD | 1.566 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.231%
African / African-American · 173/75,038 alleles
Filtering AF
0.202%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.192%
Overall
0.0117%
189/1,614,014 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.231% | 434 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| Admixed American | 0.00667% | 15,003 |
| European (non-Finnish) | 0.000254% | 393,309 |
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.Glu139=
- Coding
- c.417A>G
- MANE Select
- NM_032816
- dbSNP
- rs74954479
- Type
- single nucleotide variant
- Location
- chr19:32953690 (GRCh38)
- Gene constraint
- LOEUF 1.173 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.08
- Residue 139
- the 'disordered' region
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-glu139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown