CTSF p.Glu199=
c.597G>A · rs200932066 · VCV775294
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.115%, mid)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.024 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.41 | GERP -2.2 |
| Overall | ||
| CADD | 4.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.115%
Middle Eastern · 7/6,062 alleles
Filtering AF
0.0542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0384%
Overall
0.0207%
334/1,614,200 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.115% | 866 |
| Remaining individualsnot grpmax-eligible | 0.0352% | 2,841 |
| European (non-Finnish) | 0.0247% | 4,055 |
| Finnishnot grpmax-eligible | 0.0125% | 8,004 |
| Admixed American | 0.005% | 20,007 |
| South Asian | 0.0022% | 45,542 |
| African / African-American | 0.00133% | 75,038 |
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.Glu199=
- Coding
- c.597G>A
- MANE Select
- NM_003793
- dbSNP
- rs200932066
- Type
- single nucleotide variant
- Location
- chr11:66567256 (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.Ala22Ser Uncertain significance ★★ ⚠ same condition
- CTSF p.Arg121Pro Uncertain significance ★★ ⚠ same condition
- CTSF p.Arg196Gln Uncertain significance ★★ ⚠ same condition
- CTSF p.Arg196Trp Uncertain significance ★★ ⚠ same condition
- CTSF p.Arg205Trp Uncertain significance ★★ ⚠ same condition
- CTSF p.Arg413Cys 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-glu199 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown