CEP89 p.Ser504=
c.1512G>A · rs775600871 · VCV2723589
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, 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 1.3 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 6.746 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
South Asian · 15/90,842 alleles
Filtering AF
0.0101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00823%
Overall
0.00651%
105/1,613,060 alleles · ultra-rare
exomes 103/1,461,020 · genomes 2/152,040 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0165% | 6,056 |
| European (non-Finnish) | 0.00763% | 13,108 |
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.Ser504=
- Coding
- c.1512G>A
- MANE Select
- NM_032816
- dbSNP
- rs775600871
- Type
- single nucleotide variant
- Location
- chr19:32915390 (GRCh38)
- Gene constraint
- LOEUF 1.173 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.08
Similar variants
- CEP89 p.Ser504Leu Conflicting classifications of pathogenicity ★ ⚠ 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-ser504 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown