CTSD p.Thr87=
c.261G>A · rs372181453 · VCV137051
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.024%, afr)
Conditions
2
Inborn genetic diseases
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 -16 | GERP -3.7 |
| Overall | ||
| CADD | 0.099 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.024%
African / African-American · 18/74,910 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0128%
Overall
0.00304%
49/1,613,234 alleles · ultra-rare
exomes 39/1,461,036 · genomes 10/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.024% | 4,162 |
| Admixed American | 0.01% | 10,001 |
| South Asian | 0.0022% | 45,542 |
| European (non-Finnish) | 0.00195% | 51,301 |
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
- CTSD
- Protein
- p.Thr87=
- Coding
- c.261G>A
- MANE Select
- NM_001909
- dbSNP
- rs372181453
- Type
- single nucleotide variant
- Location
- chr11:1759607 (GRCh38)
- Gene constraint
- LOEUF 0.886 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.69 · 9 PDB
- Residue 87
- a turn; the peptidase a1 domain
Similar variants
- CTSD p.Thr87Met Uncertain significance ★★ ⚠ same residue
- CTSD c.228+1G>A Likely pathogenic ★★ same condition
- CTSD p.Glu82Ter Pathogenic/Likely pathogenic ★★ same condition
- CTSD c.828-3C>A Uncertain significance ★★ same condition
- CTSD p.Ala10Ser Uncertain significance ★★ ⚠ same condition
- CTSD p.Ala116Thr Uncertain significance ★★ ⚠ same condition
- CTSD p.Ala18Pro Uncertain significance ★★ ⚠ same condition
- CTSD p.Ala18Thr 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/ctsd-p-thr87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown