CST3 p.Leu73=
c.217C>T · VCV4702908
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00158%, nfe)
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 -10 | GERP -3 |
| Overall | ||
| CADD | 4.705 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00158%
European (non-Finnish) · 18/1,138,118 alleles
Filtering AF
0.000988%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000815%
Overall
0.00131%
18/1,374,802 alleles · very rare
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
- CST3
- Protein
- p.Leu73=
- Coding
- c.217C>T
- MANE Select
- NM_000099
- Type
- single nucleotide variant
- Location
- chr20:23637646 (GRCh38)
- Gene constraint
- LOEUF 1.912 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.56 · 11 PDB
- Residue 73
- a β-strand
Similar variants
- CST3 p.Arg71His Uncertain significance ★★ ⚠ same type
- CST3 p.His112Arg Uncertain significance ★★ ⚠ same type
- CST3 p.Met67Val Uncertain significance ★★ ⚠ same type
- CST3 p.Pro8Ser Uncertain significance ★★ ⚠ same type
- CST3 c.243+11C>T Likely benign ★★ same type
- CST3 p.Ala25Thr Benign/Likely benign ★★ same type
- CST3 p.Ala72Ser Benign ★★ ⚠ same type
- CST3 p.Arg6= Benign/Likely benign ★★ 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/cst3-p-leu73 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown