CTSA p.Ser210del
c.626CCT[1] · rs1555832780 · VCV495802
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000424%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 1.6, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,179,994 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.00031%
5/1,614,084 alleles · very rare
exomes 5/1,461,864 · genomes 0/152,220 · 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.Ser210del
- Coding
- c.626CCT[1]
- MANE Select
- NM_000308
- dbSNP
- rs1555832780
- Type
- Microsatellite
- Location
- chr20:45893243 (GRCh38)
- Gene constraint
- LOEUF 0.851 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.59 · 12 PDB
Similar variants
- CTSA p.Ser210= Likely benign ★ same residue
- CTSA p.Ser209fs Pathogenic/Likely pathogenic ★★ same type
- CTSA p.Leu18_Leu19del Benign/Likely benign ★★ same type
- CTSA p.Leu19dup Benign/Likely benign ★★ same type
- CTSA p.Pro7fs Pathogenic ★ same type
- CTSA p.Tyr395_Asn396delinsTer Pathogenic ★ same type
- CTSA p.Leu16_Leu19del Uncertain significance ★ same type
- CTSA p.Leu17_Leu19del Uncertain significance ★ 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-ser210del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown