STAG1 p.Phe178=
c.534T>C · rs768109172 · VCV2777721
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0483%, sas)
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 4.8 | GERP 0.45, phastCons 1 |
| Overall | ||
| CADD | 9.641 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0483%
South Asian · 44/91,076 alleles
Filtering AF
0.0369%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.033%
Overall
0.00297%
48/1,613,666 alleles · ultra-rare
exomes 46/1,461,512 · genomes 2/152,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0483% | 2,070 |
| Admixed American | 0.00167% | 59,956 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,478 |
| European (non-Finnish) | 0.00017% | 589,890 |
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.Phe178=
- Coding
- c.534T>C
- MANE Select
- NM_005862
- dbSNP
- rs768109172
- Type
- single nucleotide variant
- Location
- chr3:136521355 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.00 · 20 PDB
- Residue 178
- 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-phe178 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown