CTSF p.Val166=
c.498C>T · rs1590816877 · VCV747090
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. | ||
| REVEL | 0.031 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 4.148 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,028 alleles
Overall
6.84e-05%
1/1,461,860 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
- CTSF
- Protein
- p.Val166=
- Coding
- c.498C>T
- MANE Select
- NM_003793
- dbSNP
- rs1590816877
- Type
- single nucleotide variant
- Location
- chr11:66567477 (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 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-val166 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown