STUB1 p.Pro20=
c.60C>A · rs370852264 · VCV2133136
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,398,120)
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 -3.1 | GERP -3.7 |
| Overall | ||
| CADD | 6.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,398,120). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- STUB1
- Protein
- p.Pro20=
- Coding
- c.60C>A
- MANE Select
- NM_005861
- dbSNP
- rs370852264
- Type
- single nucleotide variant
- Location
- chr16:680585 (GRCh38)
- Gene constraint
- LOEUF 1.294 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.84 · 27 PDB
- Residue 20
- the 'disordered' region
Similar variants
- STUB1 p.Asn65Ser Pathogenic/Likely pathogenic ★★ same type
- STUB1 p.Tyr49Cys Pathogenic/Likely pathogenic ★★ same type
- STUB1 p.Ala11Thr Uncertain significance ★★ ⚠ same type
- STUB1 p.Arg173Leu Uncertain significance ★★ ⚠ same type
- STUB1 p.Arg35Pro Uncertain significance ★★ ⚠ same type
- STUB1 p.Asn34Ser Uncertain significance ★★ ⚠ same type
- STUB1 p.Cys48Tyr Uncertain significance ★★ same type
- STUB1 p.Glu174Gly 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/stub1-p-pro20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown