CTSF p.Leu119Pro
c.356T>C · VCV4235857
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.4972 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| AlphaMissense | 0.4972 | ambiguous |
|---|---|---|
| REVEL | 0.501 | indeterminate |
| SaProt | LLR -14.14 | damaging |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 2.3, phastCons 1 |
| Regional constraint | o/e 1.02 | unconstrained · MANE · 4,550 bp · p 0.69 · regional, not allelic |
| Overall | ||
| CADD | 24.1 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
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
- CTSF
- Protein
- p.Leu119Pro
- Coding
- c.356T>C
- MANE Select
- NM_003793
- Type
- single nucleotide variant
- Location
- chr11:66567619 (GRCh38)
- Gene constraint
- LOEUF 1.296 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.78 · 1 PDB
Similar variants
- CTSF c.1045+1G>T Likely pathogenic ★★ same condition
- CTSF p.Arg217Ter Pathogenic ★★ same condition
- CTSF p.Arg121Pro Uncertain significance ★★ ⚠ same condition
- CTSF p.Arg196Trp Uncertain significance ★★ ⚠ same condition
- CTSF p.Arg418Cys Uncertain significance ★★ ⚠ same condition
- CTSF p.Arg421Gln Uncertain significance ★★ ⚠ same condition
- CTSF p.Arg54Gly Uncertain significance ★★ ⚠ same condition
- CTSF p.Asn213Lys Uncertain significance ★★ ⚠ 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/ctsf-p-leu119pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown