STUB1 p.Ser159=
c.477C>T · rs750520142 · VCV3067400
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00644%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.39 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.2 | GERP -4.4 |
| Overall | ||
| CADD | 14.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00644%
European (non-Finnish) · 76/1,179,802 alleles
Filtering AF
0.00528%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00482%
Overall
0.00521%
84/1,611,488 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00644% | 15,524 |
| Admixed American | 0.00334% | 29,982 |
| African / African-American | 0.00267% | 37,455 |
| South Asian | 0.0022% | 45,485 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,346 |
| Finnishnot grpmax-eligible | 0.0016% | 62,686 |
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
- STUB1
- Protein
- p.Ser159=
- Coding
- c.477C>T
- MANE Select
- NM_005861
- dbSNP
- rs750520142
- Type
- single nucleotide variant
- Location
- chr16:681556 (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 159
- the 'required for interaction with mapk7' region; the 'required for interaction with and ubiquitination of myocd' region; the 'required for ubiquitination of foxo1' region; the 'required for interaction with foxo1' 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-ser159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown