SATB2 p.Ala100=
c.300G>A · rs776492115 · VCV3026190
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0121%, sas)
Conditions
1
chromosome 2q32-q33 deletion syndrome
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 -0.22 | GERP -2.5, phastCons 0.24 |
| Overall | ||
| CADD | 13.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0121%
South Asian · 11/91,084 alleles
Filtering AF
0.00676%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00522%
Overall
0.000958%
14/1,461,854 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0121% | 8,280 |
| African / African-American | 0.00133% | 74,928 |
| European (non-Finnish) | 0.000169% | 590,016 |
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
- SATB2
- Protein
- p.Ala100=
- Coding
- c.300G>A
- MANE Select
- NM_001172509
- dbSNP
- rs776492115
- Type
- single nucleotide variant
- Location
- chr2:199433384 (GRCh38)
- Gene constraint
- LOEUF 0.077 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.87 · 3 PDB
- Residue 100
- the cmp domain
Similar variants
- SATB2 c.1174-2A>G Pathogenic ★★ same condition
- SATB2 c.474-2A>G Pathogenic ★★ same condition
- SATB2 c.597+1G>A Pathogenic/Likely pathogenic ★★ same condition
- SATB2 c.700+1G>A Likely pathogenic ★★ same condition
- SATB2 p.Arg239Ter Pathogenic ★★ same condition
- SATB2 p.Arg283Ter Pathogenic ★★ same condition
- SATB2 p.Arg389Cys Pathogenic/Likely pathogenic ★★ same condition
- SATB2 p.Arg389Leu Pathogenic ★★ same condition
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/satb2-p-ala100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown