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GeneE
27 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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SATB2
SATB homeobox 2
Chromosome 2 Β· 2q33.1
NCBI Gene: 23314Ensembl: ENSG00000119042.19HGNC: HGNC:21637UniProt: B3KPQ9
195PubMed Papers
21Diseases
0Drugs
201Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
positive regulation of transcription by RNA polymerase IIRNA polymerase II transcription regulatory region sequence-specific DNA bindingprotein bindingDNA-binding transcription activator activity, RNA polymerase II-specificchromosome 2q32-q33 deletion syndromecleft palateisolated cleft palateSATB2 associated disorder
✦AI Summary

SATB2 (SATB homeobox 2) is a chr2-remodeling transcription factor that binds to matrix attachment regions (MARs) of DNA to regulate tissue-specific gene expression programs 1. The protein functions as a molecular node controlling multiple developmental processes, including osteoblast differentiation, craniofacial patterning, and palate formation 1. SATB2 acts through dual mechanisms: directly binding AT-rich DNA sequences to modulate chr2 structure, and recruiting chr2-modifying enzymes such as histone deacetylases (HDACs) and acetyltransferases (HATs) to target promoters and enhancers 12. In intestinal development, SATB2 preserves colonic stem cell identity by regulating enhancer binding of transcription factors CDX2 and HNF4A, and its loss causes stable conversion of colonic stem cells to ileal-like cells 3. In neural development, SATB2 controls callosal projection neuron identity and axon formation, with mutations causing corpus callosum agenesis 4. Clinically, SATB2 mutations cause SATB2-associated syndrome, an autosomal dominant neurodevelopmental disorder with craniofacial abnormalities and intellectual disability 5. SATB2 also functions as a tumor suppressor in lung cancer by recruiting HDAC3 to reduce histone lactylation and repress oncogene expression 2.

Sources cited
1
SATB2 binds to nuclear matrix-attachment regions and regulates osteoblast differentiation, craniofacial patterning, and palate formation
PMID: 24411565
2
SATB2 preserves colonic stem cell identity through enhancer remodeling and regulation of CDX2/HNF4A binding
PMID: 34582804
3
SATB2 controls callosal projection neuron identity and axon formation, with defects causing corpus callosum agenesis
PMID: 38718796
4
SATB2 mutations cause SATB2-associated syndrome, an autosomal dominant neurodevelopmental disorder
PMID: 31021519
5
SATB2 functions as tumor suppressor by recruiting HDAC3 to reduce histone lactylation and repress oncogene expression
PMID: 41736683
Disease Associationsβ“˜21
chromosome 2q32-q33 deletion syndromeOpen Targets
0.78Strong
cleft palateOpen Targets
0.65Moderate
isolated cleft palateOpen Targets
0.60Moderate
SATB2 associated disorderOpen Targets
0.60Moderate
genetic disorderOpen Targets
0.55Moderate
Intellectual disabilityOpen Targets
0.53Moderate
Abnormality of the skeletal systemOpen Targets
0.47Moderate
mathematical abilityOpen Targets
0.46Moderate
schizophreniaOpen Targets
0.46Moderate
Global developmental delayOpen Targets
0.42Moderate
Neurodevelopmental disorderOpen Targets
0.41Moderate
Abnormality of the dentitionOpen Targets
0.34Weak
cerebellar ataxiaOpen Targets
0.34Weak
Clinodactyly of the 5th fingerOpen Targets
0.34Weak
developmental disorder of mental healthOpen Targets
0.34Weak
DolichocephalyOpen Targets
0.34Weak
MacrocephalyOpen Targets
0.34Weak
Neurodevelopmental abnormalityOpen Targets
0.34Weak
esophageal diseaseOpen Targets
0.33Weak
colorectal cancerOpen Targets
0.33Weak
Cleft palate isolatedUniProt
Pathogenic Variants201
NM_001172509.2(SATB2):c.715C>T (p.Arg239Ter)Pathogenic
Chromosome 2q32-q33 deletion syndrome|not provided|Intellectual disability|Cleft palate|SATB2-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 239
NM_001172509.2(SATB2):c.1696G>A (p.Glu566Lys)Pathogenic
not provided|Chromosome 2q32-q33 deletion syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 566
NM_001172509.2(SATB2):c.847C>T (p.Arg283Ter)Pathogenic
Inborn genetic diseases|not provided|Chromosome 2q32-q33 deletion syndrome|SATB2 associated disorder|SATB2-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 283
NM_001172509.2(SATB2):c.1286G>A (p.Arg429Gln)Pathogenic
not provided|Chromosome 2q32-q33 deletion syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 429
NM_001172509.2(SATB2):c.1166G>T (p.Arg389Leu)Pathogenic
Chromosome 2q32-q33 deletion syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 389
NM_001172509.2(SATB2):c.1195C>T (p.Arg399Cys)Pathogenic
Chromosome 2q32-q33 deletion syndrome|Intellectual disability|not provided|SATB2 associated disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 399
NM_001172509.2(SATB2):c.1946C>T (p.Ser649Leu)Pathogenic
not provided|Inborn genetic diseases|Chromosome 2q32-q33 deletion syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 649
NM_001172509.2(SATB2):c.1728del (p.Glu577fs)Pathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 577
NM_001172509.2(SATB2):c.346G>A (p.Gly116Arg)Pathogenic
Chromosome 2q32-q33 deletion syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 116
NM_001172509.2(SATB2):c.1285C>T (p.Arg429Ter)Pathogenic
not provided|Chromosome 2q32-q33 deletion syndrome|Neurodevelopmental abnormality
β˜…β˜…β˜†β˜†2024β†’ Residue 429
NM_001172509.2(SATB2):c.808_809del (p.Gln270fs)Pathogenic
Inborn genetic diseases|Chromosome 2q32-q33 deletion syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 270
NM_001172509.2(SATB2):c.1375C>T (p.Arg459Ter)Pathogenic
Isolated cleft palate|Chromosome 2q32-q33 deletion syndrome|Dystonic disorder;Intellectual disability|not provided|Inborn genetic diseases|Neurodevelopmental disorder
β˜…β˜…β˜†β˜†2024β†’ Residue 459
NM_001172509.2(SATB2):c.1196G>A (p.Arg399His)Pathogenic
not provided|Chromosome 2q32-q33 deletion syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 399
NM_001172509.2(SATB2):c.1165C>T (p.Arg389Cys)Pathogenic
not provided|Inborn genetic diseases|Chromosome 2q32-q33 deletion syndrome|SATB2 associated disorder
β˜…β˜…β˜†β˜†2024β†’ Residue 389
NM_001172509.2(SATB2):c.1204G>A (p.Glu402Lys)Pathogenic
Chromosome 2q32-q33 deletion syndrome|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 402
NM_001172509.2(SATB2):c.1174-2A>GPathogenic
Chromosome 2q32-q33 deletion syndrome|not provided
β˜…β˜…β˜†β˜†2024
NM_001172509.2(SATB2):c.318T>G (p.Tyr106Ter)Pathogenic
Chromosome 2q32-q33 deletion syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 106
NM_001172509.2(SATB2):c.1808_1817del (p.Pro603fs)Pathogenic
Chromosome 2q32-q33 deletion syndrome|Inborn genetic diseases
β˜…β˜…β˜†β˜†2023β†’ Residue 603
NM_001172509.2(SATB2):c.1564C>T (p.Arg522Cys)Pathogenic
not provided|Chromosome 2q32-q33 deletion syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 522
NM_001172509.2(SATB2):c.1654_1655del (p.Arg552fs)Pathogenic
6 conditions|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 552
View on ClinVar β†—
Related Genes
MSL1Shared pathway100%HDGFL1Shared pathway100%HIPK4Shared pathway100%HMGB4Shared pathway100%NAA40Shared pathway100%NSD1Shared pathway100%
Tissue Expression6 tissues
Brain
100%
Liver
37%
Ovary
22%
Lung
9%
Bone Marrow
7%
Heart
6%
Gene Interaction Network
Click a node to explore
SATB2MSL1HDGFL1HIPK4HMGB4NAA40NSD1
PROTEIN STRUCTURE
Preparing viewer…
PDB1WI3 Β· NMR
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.08Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.02 [0.01–0.08]
RankingsWhere SATB2 stands among ~20K protein-coding genes
  • #2,186of 20,598
    Most Researched195 Β· top quartile
  • #336of 5,498
    Most Pathogenic Variants201 Β· top 10%
  • #20of 17,882
    Most Constrained (LOEUF)0.08 Β· top 1%
Genes detectedSATB2
Sources retrieved27 papers
Response timeβ€”
πŸ“„ Sources
27β–Ό
1
Microbiome mismatches from microbiota transplants lead to persistent off-target metabolic and immunomodulatory effects.
PMID: 40482640
Cell Β· 2025
1.00
2
SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling.
PMID: 34582804
Cell Stem Cell Β· 2022
0.90
3
USP10 promotes glioma stem cell maintenance and glioblastoma growth by antagonizing DTX3L-mediated SATB2 ubiquitination.
PMID: 41507172
Nat Commun Β· 2026
0.88
4
The role of SATB2 in skeletogenesis and human disease.
PMID: 24411565
Cytokine Growth Factor Rev Β· 2014
0.80
5
SATB2 Mediates H3K9 Delactylation by Recruiting HDAC3 to Repress LCN2 and Inhibit Lung Tumor Growth and Metastasis.
PMID: 41736683
Adv Sci (Weinh) Β· 2026
0.70