CTNS c.140+18del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
Conditions
3
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +18 | near-intronic (+18 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -2.8 |
Variant & gene context
- Gene
- CTNS
- Coding
- c.140+18del
- MANE Select
- NM_004937
- Type
- Deletion
- Location
- chr17:3647539 (GRCh38)
- Gene constraint
- LOEUF 0.754 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.27 · 6 PDB
Similar variants
- CTNS c.226del Pathogenic/Likely pathogenic ★★ same condition
- CTNS c.559_561+24del Pathogenic/Likely pathogenic ★★ same condition
- CTNS c.561+1del Pathogenic/Likely pathogenic ★★ same condition
- CTNS c.61_61+2del Pathogenic/Likely pathogenic ★★ same condition
- CTNS p.Gln108fs Pathogenic ★★ same condition
- CTNS p.Gly258fs Pathogenic ★★ same condition
- CTNS p.His105fs Pathogenic ★★ same condition
- CTNS p.Phe9fs Pathogenic/Likely 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/ctns-c-140-plus-18del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown