CTSA p.Glu354=
c.1062G>A · rs1568765243 · VCV632781
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
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 1.9 | GERP -0.35, phastCons 1 |
| Overall | ||
| CADD | 5.576 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,024 alleles
Overall
0.000657%
1/152,166 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
- CTSA
- Protein
- p.Glu354=
- Coding
- c.1062G>A
- MANE Select
- NM_000308
- dbSNP
- rs1568765243
- Type
- single nucleotide variant
- Location
- chr20:45895107 (GRCh38)
- Gene constraint
- LOEUF 0.851 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.59 · 12 PDB
- Residue 354
- a disulfide bond
Similar variants
- CTSA p.Glu354Lys Uncertain significance ★ ⚠ same residue
- CTSA c.1-2A>G Pathogenic/Likely pathogenic ★★ same type
- CTSA c.358-2A>G Likely pathogenic ★★ same type
- CTSA c.601-2A>G Pathogenic/Likely pathogenic ★★ same type
- CTSA c.692+3A>G Pathogenic ★★ same type
- CTSA c.948+1G>A Likely pathogenic ★★ same type
- CTSA p.Arg375Ter Pathogenic/Likely pathogenic ★★ same type
- CTSA p.Cys256Ter Pathogenic/Likely pathogenic ★★ same type
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-glu354 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown