CTSC p.Leu16fs
c.45del · VCV3755323
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
3
periodontitis, aggressive
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 7 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.22 | GERP -2.7, phastCons 0.003 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CTSC
- Protein
- p.Leu16fs
- Coding
- c.45del
- MANE Select
- NM_001814
- Type
- Deletion
- Location
- chr11:88337628 (GRCh38)
- Gene constraint
- LOEUF 1.051 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.64 · 18 PDB
Similar variants
- CTSC p.Leu16= Likely benign ★ same residue
- CTSC p.Leu381fs Pathogenic ★★ same condition
- CTSC p.Lys63_Val64insTer Pathogenic/Likely pathogenic ★★ same condition
- CTSC p.Thr189fs Pathogenic ★★ same condition
- CTSC c.173-7del Benign/Likely benign ★★ same condition
- CTSC c.486-25_492del Likely pathogenic ★ same condition
- CTSC p.Ala417fs Pathogenic ★ same condition
- CTSC p.Asp236fs Pathogenic ★ 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/ctsc-p-leu16fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown