CTSC p.Lys70=
c.210G>A · rs771971698 · VCV2190043
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00404%, afr)
Conditions
3
periodontitis, aggressive
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.101 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -1.8, phastCons 0.93 |
| Overall | ||
| CADD | 11.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00404%
African / African-American · 3/74,278 alleles
Filtering AF
0.00107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000497%
Overall
0.000311%
5/1,606,140 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00404% | 24,759 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,248 |
| European (non-Finnish) | 8.52e-05% | 1,173,949 |
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
- CTSC
- Protein
- p.Lys70=
- Coding
- c.210G>A
- MANE Select
- NM_001814
- dbSNP
- rs771971698
- Type
- single nucleotide variant
- Location
- chr11:88335045 (GRCh38)
- Gene constraint
- LOEUF 1.051 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.64 · 18 PDB
- Residue 70
- a disulfide bond; a UniProt-annotated variant site (in pls); a turn
Similar variants
- CTSC c.319-1G>A Pathogenic ★★ same condition
- CTSC c.757+1G>T Likely pathogenic ★★ same condition
- CTSC c.-55C>A Pathogenic ★★ same condition
- CTSC p.Arg210Ter Pathogenic ★★ same condition
- CTSC p.Arg250Ter Pathogenic/Likely pathogenic ★★ same condition
- CTSC p.Arg272His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CTSC p.Arg272Pro Pathogenic/Likely pathogenic ★★ same condition
- CTSC p.Arg339Cys Pathogenic/Likely pathogenic ★★ ⚠ 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/ctsc-p-lys70 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown