SATB2

Chr 2q33.1

SATB homeobox 2

Aliases:: KIAA1034, FLJ21474
MANE:: ENST00000417098.6

OMIM: 608148 ↗NCBI: 23314 ↗Ensembl ↗

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Predicted protein structure

AlphaFold predicted structure

SATB2 · Q9UPW6

v62025-08-01

Predicted Aligned Error matrix for SATB2 — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

66.1/ 100

Low

733 residues

Confidence breakdown

Very high(≥ 90)29%
Confident(70–90)24%
Low(50–70)7%
Very low(< 50)40%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

Clefting
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
DDG2P
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Early onset or syndromic epilepsy
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Fetal anomalies
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Intellectual disability
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Disease associations (Open Targets)

chromosome 2q32-q33 deletion syndrome
0.78
cleft palate
0.67
Intellectual disability
0.62
isolated cleft palate
0.60
SATB2 associated disorder
0.60
hereditary disease
0.55
Abnormality of the skeletal system
0.47
schizophrenia
0.47
mathematical ability
0.47
Global developmental delay
0.42

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

DNA-binding protein SATB2

Binds to DNA, at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double-stranded DNA. Transcription factor controlling nuclear gene expression, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes and also by recruiting corepressors (HDACs) or coactivators (HATs) directly to promoters and enhancers. Required for the initiation of the upper-layer neurons (UL1) specific genetic program and for the inactivation of deep-layer neurons (DL) and UL2 specific genes, probably by modulating BCL11B expression. Repressor of Ctip2 and regulatory determinant of corticocortical connections in the developing cerebral cortex. May play an important role in palate formation. Acts as a molecular node in a transcriptional network regulating skeletal development and osteoblast differentiation