CTSK p.Val119=
c.357C>T · rs142306783 · VCV788324
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0441%, 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 | GERP -3.9 |
| Overall | ||
| CADD | 5.097 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0441%
African / African-American · 33/74,892 alleles
Filtering AF
0.0322%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0281%
Overall
0.01%
162/1,613,962 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0441% | 2,269 |
| East Asian | 0.0134% | 7,483 |
| European (non-Finnish) | 0.00966% | 10,351 |
| Finnishnot grpmax-eligible | 0.00625% | 16,002 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| Admixed American | 0.00167% | 59,990 |
| South Asian | 0.0011% | 91,068 |
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
- CTSK
- Protein
- p.Val119=
- Coding
- c.357C>T
- MANE Select
- NM_000396
- dbSNP
- rs142306783
- Type
- single nucleotide variant
- Location
- chr1:150805903 (GRCh38)
- Gene constraint
- LOEUF 0.748 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.89 · 70 PDB
Similar variants
- CTSK c.121-1G>A Pathogenic/Likely pathogenic ★★ same type
- CTSK c.121-2A>G Pathogenic/Likely pathogenic ★★ same type
- CTSK c.244-29A>G Pathogenic/Likely pathogenic ★★ same type
- CTSK c.244-2A>C Likely pathogenic ★★ same type
- CTSK c.400-1G>C Likely pathogenic ★★ same type
- CTSK c.784+1G>A Likely pathogenic ★★ same type
- CTSK p.Ala277Val Pathogenic ★★ same type
- CTSK p.Arg122Ter Pathogenic/Likely pathogenic ★★ 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/ctsk-p-val119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown