CTSF p.Ala140=
c.420C>T · rs149140177 · VCV3037581
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.028%, afr)
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 1.1 | GERP -3.5, phastCons 0.002 |
| Overall | ||
| CADD | 8.985 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.028%
African / African-American · 21/74,940 alleles
Filtering AF
0.0187%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0157%
Overall
0.00155%
25/1,614,100 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.028% | 3,569 |
| Admixed American | 0.00333% | 30,002 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,245 |
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.Ala140=
- Coding
- c.420C>T
- MANE Select
- NM_003793
- dbSNP
- rs149140177
- Type
- single nucleotide variant
- Location
- chr11:66567555 (GRCh38)
- Gene constraint
- LOEUF 1.296 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.78 · 1 PDB
Similar variants
- CTSF p.Ala140Thr Benign ★★ same residue
- 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
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-ala140 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown