CTSF p.Thr353=
c.1059A>G · rs1590815329 · VCV735369
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,569,432)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.036 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -7 | GERP -4.3 |
| Overall | ||
| CADD | 1.754 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,569,432). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CTSF
- Protein
- p.Thr353=
- Coding
- c.1059A>G
- MANE Select
- NM_003793
- dbSNP
- rs1590815329
- Type
- single nucleotide variant
- Location
- chr11:66564993 (GRCh38)
- Gene constraint
- LOEUF 1.296 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.78 · 1 PDB
- Residue 353
- a disulfide bond
Similar variants
- CTSF c.1045+1G>T Likely pathogenic ★★ same type
- CTSF p.Arg217Ter Pathogenic ★★ same type
- CTSF p.Ala22Ser Uncertain significance ★★ ⚠ same type
- CTSF p.Arg121Pro Uncertain significance ★★ ⚠ same type
- CTSF p.Arg196Gln Uncertain significance ★★ ⚠ same type
- CTSF p.Arg196Trp Uncertain significance ★★ ⚠ same type
- CTSF p.Arg205Trp Uncertain significance ★★ ⚠ same type
- CTSF p.Arg413Cys Uncertain significance ★★ ⚠ 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/ctsf-p-thr353 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown