CEP55 p.Asp53=
c.159T>C · VCV3665364
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.569%, afr)
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 -0.36 | GERP -3, phastCons 0.17 |
| Overall | ||
| CADD | 4.331 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.569%
African / African-American · 426/74,872 alleles
Filtering AF
0.524%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.507%
Overall
0.0299%
482/1,612,474 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.569% | 176 |
| Admixed American | 0.0471% | 2,122 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,469 |
| South Asian | 0.0011% | 90,784 |
| European (non-Finnish) | 0.000763% | 131,065 |
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.Asp53=
- Coding
- c.159T>C
- MANE Select
- NM_018131
- Type
- single nucleotide variant
- Location
- chr10:93500210 (GRCh38)
- Gene constraint
- LOEUF 1.138 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.85 · 4 PDB
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-asp53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown