CEP55 p.Ala423=
c.1269C>T · rs781021700 · VCV758695
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0171%, nfe)
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 -0.65 | GERP -3.2 |
| Overall | ||
| CADD | 1.934 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0171%
European (non-Finnish) · 202/1,179,976 alleles
Filtering AF
0.0152%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0144%
Overall
0.013%
209/1,613,826 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0171% | 5,841 |
| South Asian | 0.00549% | 18,215 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
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
- CEP55
- Protein
- p.Ala423=
- Coding
- c.1269C>T
- MANE Select
- NM_018131
- dbSNP
- rs781021700
- Type
- single nucleotide variant
- Location
- chr10:93528027 (GRCh38)
- Gene constraint
- LOEUF 1.138 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.85 · 4 PDB
- Residue 423
- a UniProt-annotated variant site (in march); the 'required for localization to the interphase centrosome and to the midbody during cytokinesis' region
Similar variants
- CEP55 p.Arg64Ter Pathogenic/Likely pathogenic ★★ same type
- CEP55 p.Arg86Ter Pathogenic ★★ same type
- CEP55 p.Ser425Ter Pathogenic ★★ same type
- CEP55 p.Arg385Gln Uncertain significance ★★ ⚠ same type
- CEP55 p.His293Arg Uncertain significance ★★ ⚠ same type
- CEP55 p.Pro426Arg Uncertain significance ★★ ⚠ same type
- CEP55 p.Ser2Phe Uncertain significance ★★ ⚠ same type
- CEP55 p.Val127Ile 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/cep55-p-ala423 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown