CTSF p.Gly258Ser
c.772G>A · rs1448373102 · VCV1311252
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0756 | likely benign |
|---|---|---|
| REVEL | 0.005 | strongly benign-leaning |
| SaProt | LLR -3.05 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.7 | GERP -4.3 |
| Regional constraint | o/e 1.02 | unconstrained · MANE · 4,550 bp · p 0.69 · regional, not allelic |
| Overall | ||
| CADD | 0.246 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,927 |
| East Asiangrpmax | 0.00446% | 22,446 |
Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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.Gly258Ser
- Coding
- c.772G>A
- MANE Select
- NM_003793
- dbSNP
- rs1448373102
- Type
- single nucleotide variant
- Location
- chr11:66566117 (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-gly258ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown