CEP63 p.Arg540=
c.1620G>A · rs140668390 · VCV434749
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.545%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.046 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.12 | GERP -3.5, phastCons 0.001 |
| Overall | ||
| CADD | 4.228 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.545%
Middle Eastern · 33/6,058 alleles
Filtering AF
0.399%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.363%
Overall
0.0719%
1,160/1,613,808 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.545% | 184 |
| South Asian | 0.411% | 244 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| Remaining individualsnot grpmax-eligible | 0.0896% | 1,116 |
| European (non-Finnish) | 0.0562% | 1,780 |
| Admixed American | 0.0383% | 2,609 |
| African / African-American | 0.00933% | 10,715 |
| Finnishnot grpmax-eligible | 0.00156% | 63,978 |
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.Arg540=
- Coding
- c.1620G>A
- MANE Select
- NM_001353108
- dbSNP
- rs140668390
- Type
- single nucleotide variant
- Location
- chr3:134558294 (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-arg540 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown