SATB1 p.Pro462=
c.1386C>A · rs2229261 · VCV1230415
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 93.6%, eas) — too common for a highly-penetrant pathogenic allele
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 -2.5 | GERP -3.9 |
| Overall | ||
| CADD | 3.874 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
93.6%
East Asian · 41,978/44,852 alleles
Filtering AF
92.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 92.5%
Overall
60.7%
979,609/1,613,252 alleles · common
exomes 888,032/1,461,452 · genomes 91,577/151,800 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 93.6% | 1 |
| Admixed American | 76.4% | 1 |
| South Asian | 69.5% | 1 |
| Remaining individualsnot grpmax-eligible | 61.3% | 2 |
| Amishnot grpmax-eligible | 60.6% | 2 |
| European (non-Finnish) | 58.8% | 2 |
| African / African-American | 57.9% | 2 |
| Middle Eastern | 56.6% | 2 |
| Finnishnot grpmax-eligible | 53.7% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 52.6% | 2 |
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
- SATB1
- Protein
- p.Pro462=
- Coding
- c.1386C>A
- MANE Select
- NM_002971
- dbSNP
- rs2229261
- Type
- single nucleotide variant
- Location
- chr3:18386432 (GRCh38)
- Gene constraint
- LOEUF 0.209 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.88 · 8 PDB
- Residue 462
- a UniProt-annotated variant site (in defda; reduced transcriptional repression)
Similar variants
- SATB1 p.Pro462His Uncertain significance ★ ⚠ same residue
- SATB1 p.Arg427Gln Likely pathogenic ★★ ⚠ same type
- SATB1 p.Arg553Ter Pathogenic ★★ same type
- SATB1 p.Arg642Ter Pathogenic ★★ same type
- SATB1 p.Glu407Gln Pathogenic ★★ same type
- SATB1 p.Glu530Lys Pathogenic/Likely pathogenic ★★ same type
- SATB1 p.Arg380His Uncertain significance ★★ ⚠ same type
- SATB1 p.Arg627Gln Uncertain significance ★★ ⚠ 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/satb1-p-pro462 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown