STAG1 p.Ser487=
c.1461T>C · rs986075585 · VCV2907482
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.3 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.6 | GERP -3.9, phastCons 1 |
| Overall | ||
| CADD | 8.226 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,892 alleles
Overall
0.000186%
3/1,612,994 alleles · very rare
exomes 3/1,460,728 · genomes 0/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,892 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,464 |
| European (non-Finnish) | 8.48e-05% | 1,179,569 |
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
- STAG1
- Protein
- p.Ser487=
- Coding
- c.1461T>C
- MANE Select
- NM_005862
- dbSNP
- rs986075585
- Type
- single nucleotide variant
- Location
- chr3:136443372 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.00 · 20 PDB
- Residue 487
- 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-ser487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown