CEP89 p.Ala707=
c.2121G>A · rs533496556 · VCV2171099
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0411%, 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 -20 | GERP -3.7 |
| Overall | ||
| CADD | 1.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0411%
South Asian · 37/90,058 alleles
Filtering AF
0.0306%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.027%
Overall
0.00393%
63/1,602,776 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0411% | 2,434 |
| Admixed American | 0.0117% | 8,525 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,159 |
| European (non-Finnish) | 0.00136% | 73,666 |
| African / African-American | 0.00133% | 75,022 |
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.Ala707=
- Coding
- c.2121G>A
- MANE Select
- NM_032816
- dbSNP
- rs533496556
- Type
- single nucleotide variant
- Location
- chr19:32881858 (GRCh38)
- Gene constraint
- LOEUF 1.173 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.08
Similar variants
- CEP89 p.Ala707Val Uncertain significance ★ ⚠ 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
- CEP89 p.Arg102Trp 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-ala707 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown