CEP63 p.Leu654=
c.1960T>C · rs2110178407 · VCV1577832
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.28 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.3 | GERP -3.8 |
| Overall | ||
| CADD | 1.127 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CEP63
- Protein
- p.Leu654=
- Coding
- c.1960T>C
- MANE Select
- NM_001353108
- dbSNP
- rs2110178407
- Type
- single nucleotide variant
- Location
- chr3:134561383 (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-leu654 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown