CTSK p.Pro327=
c.981C>T · rs2101945934 · VCV1530822
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.49e-05%, 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 2.1 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 9.458 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.49e-05%
European (non-Finnish) · 1/1,178,422 alleles
Overall
6.85e-05%
1/1,460,090 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.Pro327=
- Coding
- c.981C>T
- MANE Select
- NM_000396
- dbSNP
- rs2101945934
- Type
- single nucleotide variant
- Location
- chr1:150796808 (GRCh38)
- Gene constraint
- LOEUF 0.748 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.89 · 70 PDB
- Residue 327
- a β-strand
Similar variants
- 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
- CTSK p.Ala277Val Pathogenic ★★ same type
- CTSK p.Arg122Ter Pathogenic/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-pro327 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown