CTSA p.Asp106=
c.318T>C · rs753072437 · VCV2652352
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000254%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP 1.9, phastCons 0.001 |
| Overall | ||
| CADD | 10.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,180,038 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000186%
3/1,614,000 alleles · very rare
exomes 2/1,461,808 · genomes 1/152,192 · joint denominator
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
- CTSA
- Protein
- p.Asp106=
- Coding
- c.318T>C
- MANE Select
- NM_000308
- dbSNP
- rs753072437
- Type
- single nucleotide variant
- Location
- chr20:45892284 (GRCh38)
- Gene constraint
- LOEUF 0.851 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.59 · 12 PDB
Similar variants
- CTSA c.1-2A>G Pathogenic/Likely pathogenic ★★ same type
- CTSA c.358-2A>G Likely pathogenic ★★ same type
- CTSA c.601-2A>G Pathogenic/Likely pathogenic ★★ same type
- CTSA c.692+3A>G Pathogenic ★★ same type
- CTSA c.948+1G>A Likely pathogenic ★★ same type
- CTSA p.Arg375Ter Pathogenic/Likely pathogenic ★★ same type
- CTSA p.Cys256Ter Pathogenic/Likely pathogenic ★★ same type
- CTSA p.Cys281Ter 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/ctsa-p-asp106 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown