CTNS p.Tyr281=
c.843T>C · rs2076200273 · VCV1127912
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
3
Inborn genetic diseases
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 0.24 | GERP -1.9, phastCons 0.99 |
| Overall | ||
| CADD | 6.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CTNS
- Protein
- p.Tyr281=
- Coding
- c.843T>C
- MANE Select
- NM_004937
- dbSNP
- rs2076200273
- Type
- single nucleotide variant
- Location
- chr17:3658166 (GRCh38)
- Gene constraint
- LOEUF 0.754 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.27 · 6 PDB
- Residue 281
- an α-helix; the pq-loop 2 domain; a binding site
Similar variants
- CTNS p.Tyr281fs Pathogenic/Likely pathogenic ★★ same residue
- 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
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-p-tyr281 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown