CSTB p.Lys56=
c.168G>A · rs386833440 · VCV55958
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Unverricht-Lundborg syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.78 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.76 | loss · gain 0.68 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.1 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 23.7 | 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
- CSTB
- Protein
- p.Lys56=
- Coding
- c.168G>A
- MANE Select
- NM_000100
- dbSNP
- rs386833440
- Type
- single nucleotide variant
- Location
- chr21:43774658 (GRCh38)
- Gene constraint
- LOEUF 1.681 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 95.81 · 3 PDB
- Residue 56
- a β-strand
Disease context
Unverricht-Lundborg syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Progressive myoclonic epilepsy type 1 (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Childhood
- Prevalence
- 1-9 / 100 000 (Finland)
Similar variants
- CSTB p.Lys56Arg Uncertain significance ★★ ⚠ same residue
- CSTB c.67-1G>C Pathogenic ★★ same condition
- CSTB p.Arg68Ter Pathogenic ★★ same condition
- CSTB p.Gln22Ter Pathogenic/Likely pathogenic ★★ same condition
- CSTB p.Gln46Ter Pathogenic/Likely pathogenic ★★ same condition
- CSTB p.Tyr53Cys Uncertain significance ★★ ⚠ same condition
- CSTB p.Val57Leu Uncertain significance ★★ ⚠ same condition
- CSTB c.67-3T>C Benign/Likely benign ★★ 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/cstb-p-lys56 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown