CTNS c.61+19C>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.5e-05%, nfe)
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 +19 | near-intronic (+19 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.76 | GERP -2.9 |
| Overall | ||
| CADD | 2.682 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.5e-05%
European (non-Finnish) · 1/1,176,824 alleles
Overall
6.86e-05%
1/1,458,320 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
- CTNS
- Coding
- c.61+19C>A
- MANE Select
- NM_004937
- Type
- single nucleotide variant
- Location
- chr17:3640286 (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.140+1G>T Pathogenic/Likely pathogenic ★★ same condition
- CTNS c.140+2T>C Pathogenic/Likely pathogenic ★★ same condition
- CTNS c.141-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CTNS c.141-24T>C Pathogenic ★★ same condition
- CTNS c.225+3A>T Pathogenic/Likely pathogenic ★★ same condition
- CTNS c.225+5G>A Likely pathogenic ★★ same condition
- CTNS c.61+2T>C Likely pathogenic ★★ same condition
- CTNS c.61+5G>A 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-61-plus-19c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown