CTSA p.Asp408fs
c.1223dup · VCV3893081
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
galactosialidosis
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 13 of 15 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.8, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CTSA
- Protein
- p.Asp408fs
- Coding
- c.1223dup
- MANE Select
- NM_000308
- Type
- Duplication
- Location
- chr20:45897774 (GRCh38)
- Gene constraint
- LOEUF 0.851 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.59 · 12 PDB
- Residue 408
- an α-helix
Disease context
galactosialidosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Galactosialidosis (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- All ages
Similar variants
- CTSA p.Gln369fs Pathogenic ★★ same condition
- CTSA p.Tyr340Ter Pathogenic/Likely pathogenic ★★ same condition
- CTSA p.Pro86fs Pathogenic ★ same condition
- CTSA c.195-7dup Benign ★ same condition
- CTSA c.1-2A>G Pathogenic/Likely pathogenic ★★ same condition
- CTSA c.358-2A>G Likely pathogenic ★★ same condition
- CTSA c.445-18_447del Likely pathogenic ★★ same condition
- CTSA c.601-2A>G 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/ctsa-p-asp408fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown