CEP63 p.Val189=
c.567C>A · rs146845434 · VCV128710
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.6%, eas)
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 2.7 | GERP 1.9, phastCons 0.99 |
| Overall | ||
| CADD | 8.662 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.6%
East Asian · 1,168/44,864 alleles
Filtering AF
2.48%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.43%
Overall
0.0848%
1,368/1,613,578 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.6% | 38 |
| Remaining individualsnot grpmax-eligible | 0.25% | 401 |
| South Asian | 0.0198% | 5,058 |
| Admixed American | 0.0133% | 7,503 |
| African / African-American | 0.00933% | 10,717 |
| European (non-Finnish) | 0.000933% | 107,232 |
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
- CEP63
- Protein
- p.Val189=
- Coding
- c.567C>A
- MANE Select
- NM_001353108
- dbSNP
- rs146845434
- Type
- single nucleotide variant
- Location
- chr3:134545597 (GRCh38)
- Gene constraint
- LOEUF 1.127 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.95 · 4 PDB
Similar variants
- CEP63 c.1067+2T>C Likely pathogenic ★★ same type
- CEP63 c.790-2A>G Likely pathogenic ★★ same type
- CEP63 p.Arg150His Uncertain significance ★★ ⚠ same type
- CEP63 p.Arg215Trp Uncertain significance ★★ ⚠ same type
- CEP63 p.Arg229Cys Uncertain significance ★★ ⚠ same type
- CEP63 p.Arg312Gln Uncertain significance ★★ ⚠ same type
- CEP63 p.Arg46His Uncertain significance ★★ ⚠ same type
- CEP63 p.Arg474His 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/cep63-p-val189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown