CEP63 p.Ser586=
c.1758G>A · VCV3611593
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, 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 0.52 | GERP -3.1, phastCons 0.028 |
| Overall | ||
| CADD | 9.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
East Asian · 5/44,892 alleles
Filtering AF
0.00434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00286%
Overall
0.00347%
56/1,613,956 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0111% | 8,978 |
| European (non-Finnish) | 0.00415% | 24,082 |
| Admixed American | 0.00167% | 59,976 |
| African / African-American | 0.00134% | 74,876 |
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.Ser586=
- Coding
- c.1758G>A
- MANE Select
- NM_001353108
- Type
- single nucleotide variant
- Location
- chr3:134559234 (GRCh38)
- Gene constraint
- LOEUF 1.127 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.95 · 4 PDB
Similar variants
- CEP63 p.Ser586Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-ser586 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown