STUB1 p.Glu5=
c.15G>A · rs778376720 · VCV1913883
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0105%, amr)
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 4.7 | GERP -3.5, phastCons 1 |
| Overall | ||
| CADD | 14.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0105%
Admixed American · 3/28,682 alleles
Filtering AF
0.00277%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00147%
Overall
0.000339%
4/1,180,782 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0105% | 9,561 |
| European (non-Finnish) | 9.67e-05% | 1,033,802 |
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.Glu5=
- Coding
- c.15G>A
- MANE Select
- NM_005861
- dbSNP
- rs778376720
- Type
- single nucleotide variant
- Location
- chr16:680540 (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 5
- the 'disordered' region
Similar variants
- STUB1 p.Glu5Lys Uncertain significance ★ ⚠ same residue
- 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
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-glu5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown