CEP57 p.Leu397=
c.1189T>C · VCV3831966
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.19 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.21 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 8.177 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,960 alleles
Overall
6.84e-05%
1/1,461,846 alleles · very rare
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
- CEP57
- Protein
- p.Leu397=
- Coding
- c.1189T>C
- MANE Select
- NM_014679
- Type
- single nucleotide variant
- Location
- chr11:95829248 (GRCh38)
- Gene constraint
- LOEUF 0.74 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.32 · 3 PDB
- Residue 397
- an α-helix; the 'mediates interaction with microtubules' region
Similar variants
- CEP57 p.Leu397Val Uncertain significance ★ ⚠ same residue
- CEP57 p.Ala19Gly Uncertain significance ★★ ⚠ same condition
- CEP57 p.Ala278Thr Uncertain significance ★★ ⚠ same condition
- CEP57 p.Ala412Thr Uncertain significance ★★ ⚠ same condition
- CEP57 p.Ala4Gly Uncertain significance ★★ ⚠ same condition
- CEP57 p.Ala4Val Uncertain significance ★★ ⚠ same condition
- CEP57 p.Ala68Val Uncertain significance ★★ ⚠ same condition
- CEP57 p.Arg175Gln Uncertain significance ★★ ⚠ same condition
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/cep57-p-leu397 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown