CTSK p.Lys52=
c.156A>G · rs1571127681 · VCV796135
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.84e-05%)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | acceptor gain, 35 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.38 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 9.085 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.84e-05%
Overall
6.84e-05%
1/1,461,852 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
- CTSK
- Protein
- p.Lys52=
- Coding
- c.156A>G
- MANE Select
- NM_000396
- dbSNP
- rs1571127681
- Type
- single nucleotide variant
- Location
- chr1:150806189 (GRCh38)
- Gene constraint
- LOEUF 0.748 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.89 · 70 PDB
- Residue 52
- an α-helix
Similar variants
- CTSK p.Lys52Glu Uncertain significance ★ ⚠ same residue
- CTSK p.Lys52Ter Pathogenic same residue
- CTSK c.121-1G>A Pathogenic/Likely pathogenic ★★ same type
- CTSK c.121-2A>G Pathogenic/Likely pathogenic ★★ same type
- CTSK c.244-29A>G Pathogenic/Likely pathogenic ★★ same type
- CTSK c.244-2A>C Likely pathogenic ★★ same type
- CTSK c.400-1G>C Likely pathogenic ★★ same type
- CTSK c.784+1G>A Likely pathogenic ★★ 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/ctsk-p-lys52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown