SATB2 p.Pro578=
c.1734G>A · rs937895148 · VCV1586541
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.1 | GERP -4.9 |
| Overall | ||
| CADD | 0.772 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00157%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00134%
Overall
0.00235%
38/1,613,832 alleles · ultra-rare
exomes 35/1,461,734 · genomes 3/152,098 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0101% | 9,868 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,620 |
| European (non-Finnish) | 0.00229% | 43,701 |
| South Asian | 0.0022% | 45,535 |
| Admixed American | 0.00167% | 59,984 |
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.Pro578=
- Coding
- c.1734G>A
- MANE Select
- NM_001172509
- dbSNP
- rs937895148
- Type
- single nucleotide variant
- Location
- chr2:199308766 (GRCh38)
- Gene constraint
- LOEUF 0.077 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.87 · 3 PDB
Similar variants
- SATB2 p.Pro578Thr Benign/Likely benign ★★ same residue
- 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
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-pro578 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown