STAG1 p.Glu306Gln
c.916G>C · VCV4795299
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.9853 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
2/3 damaging
AlphaMissense, REVEL, SaProt
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9853 | likely pathogenic |
|---|---|---|
| REVEL | 0.249 | benign-leaning |
| SaProt | LLR -13.16 | damaging |
| ⇒ AlphaMissense and SaProt call this damaging; REVEL does not. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 7.8, phastCons 1 |
| Regional constraint | o/e 0.36 | unconstrained · MANE · 48 kb · p 1.1e-15 · regional, not allelic |
| Overall | ||
| CADD | 28.8 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- STAG1
- Protein
- p.Glu306Gln
- Coding
- c.916G>C
- MANE Select
- NM_005862
- Type
- single nucleotide variant
- Location
- chr3:136477399 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.00 · 20 PDB
- Residue 306
- the scd domain; an α-helix
Similar variants
- STAG1 c.1026+2T>C Likely pathogenic ★★ same type
- STAG1 p.Arg140Ter Pathogenic/Likely pathogenic ★★ same type
- STAG1 p.Arg216Gly Pathogenic/Likely pathogenic ★★ same type
- STAG1 p.Arg373Gln Pathogenic/Likely pathogenic ★★ same type
- STAG1 p.Arg373Ter Pathogenic/Likely pathogenic ★★ same type
- STAG1 p.Arg377Cys Pathogenic/Likely pathogenic ★★ same type
- STAG1 p.Arg395Ter Likely pathogenic ★★ same type
- STAG1 p.Arg971Ter Pathogenic/Likely pathogenic ★★ 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/stag1-p-glu306gln (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown