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GeneE
27 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SATB1
SATB homeobox 1
Chromosome 3 Β· 3p24.3
NCBI Gene: 6304Ensembl: ENSG00000182568.19HGNC: HGNC:10541UniProt: Q01826
231PubMed Papers
22Diseases
0Drugs
35Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
RESEARCH IMPACT
Trending
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingsequence-specific DNA bindingnucleusnegative regulation of transcription by RNA polymerase IIdevelopmental delay with dysmorphic facies and dental anomaliesKohlschutter-Tonz syndrome-likegenetic disorderatopic eczema
✦AI Summary

SATB1 (SATB homeobox 1) is a chr3-organizing transcription factor that functions as a sequence-specific DNA repressor binding AT-rich regulatory elements 1. It acts as a genomic organizer controlling nuclear architecture through chr3 remodeling by recruiting corepressors and coactivators to matrix attachment regions 2. Mechanistically, SATB1 regulates chr3 accessibility and transcriptional programs through phosphorylation and acetylation-dependent mechanisms 3. It functions as an accessory transcription factor in regulatory T cell (Treg) development, working with FOXP3 and other factors to specify Treg cell identity and function 45. SATB1 is essential for maintaining stem-like CD8+ T cell properties including quiescence and multipotency during chr3 infection, regulating stemness-associated genes such as Tcf7, Bach2, and Myb 3. Additionally, TGF-Ξ²-mediated SATB1 silencing promotes T follicular helper cell differentiation and tertiary lymphoid structure formation in tumors 2. Disease relevance is significant: mutations in SATB1 cause distinct neurodevelopmental disorders, with missense variants in DNA-binding domains producing severe phenotypes through increased transcriptional repression, while haploinsufficient variants cause milder presentations 1. SATB1 dysfunction impairs Treg development, contributing to autoimmune disease pathogenesis 6. In cancer, high SATB1 expression in colorectal cancer promotes disease progression and associates with poor prognosis 7.

Sources cited
1
SATB1 is an accessory transcription factor of the CUT homeobox family that controls Treg cell identity
PMID: 37336954
2
SATB1 mutations impair Treg development and contribute to autoimmune disease pathogenesis
PMID: 33537838
3
Different SATB1 variant types cause distinct neurodevelopmental disorders with specific pathophysiological mechanisms; missense variants in DNA-binding domains increase transcriptional repression, while haploinsufficient variants produce milder phenotypes
PMID: 33513338
4
TGF-Ξ²-mediated SATB1 silencing promotes T follicular helper cell differentiation and tertiary lymphoid structure formation in tumors
PMID: 35021053
5
SATB1 is essential for maintaining stem-like CD8+ T cell quiescence and regulates stemness-associated genes including Tcf7, Bach2, and Myb through chromatin accessibility and transcriptional control
PMID: 40847243
6
SATB1 coregulates a gene network with HIVEP2 in human Treg cells important for immunosuppression
PMID: 32989329
7
High SATB1 expression in colorectal cancer facilitates disease progression and is associated with poor prognosis
PMID: 25543122
Disease Associationsβ“˜22
developmental delay with dysmorphic facies and dental anomaliesOpen Targets
0.67Moderate
Kohlschutter-Tonz syndrome-likeOpen Targets
0.66Moderate
genetic disorderOpen Targets
0.50Moderate
atopic eczemaOpen Targets
0.48Moderate
Neurodevelopmental disorderOpen Targets
0.46Moderate
developmental disorder of mental healthOpen Targets
0.42Moderate
Intellectual disabilityOpen Targets
0.37Weak
complex neurodevelopmental disorderOpen Targets
0.37Weak
Eczematoid dermatitisOpen Targets
0.37Weak
Neurodevelopmental delayOpen Targets
0.36Weak
nerve plexus diseaseOpen Targets
0.34Weak
Abruptio PlacentaeOpen Targets
0.33Weak
dermatitisOpen Targets
0.32Weak
ovarian neoplasmOpen Targets
0.31Weak
response to antihypertensive drugOpen Targets
0.30Weak
anxiety disorderOpen Targets
0.29Weak
Crohn's diseaseOpen Targets
0.28Weak
hypertensionOpen Targets
0.26Weak
type 2 diabetes mellitusOpen Targets
0.26Weak
smoking initiationOpen Targets
0.26Weak
Den Hoed-de Boer-Voisin syndromeUniProt
Developmental delay with dysmorphic facies and dental anomaliesUniProt
Pathogenic Variants35
NM_002971.6(SATB1):c.431dup (p.Tyr144Ter)Likely pathogenic
Developmental delay with dysmorphic facies and dental anomalies
β˜…β˜…β˜†β˜†2025β†’ Residue 144
NM_002971.6(SATB1):c.1280G>A (p.Arg427Gln)Likely pathogenic
not specified|Kohlschutter-Tonz syndrome-like
β˜…β˜…β˜†β˜†2025β†’ Residue 427
NM_002971.6(SATB1):c.1924C>T (p.Arg642Ter)Pathogenic
not provided|Developmental delay with dysmorphic facies and dental anomalies
β˜…β˜…β˜†β˜†2024β†’ Residue 642
NM_002971.6(SATB1):c.1219G>C (p.Glu407Gln)Pathogenic
Kohlschutter-Tonz syndrome-like|Developmental delay with dysmorphic facies and dental anomalies
β˜…β˜…β˜†β˜†2024β†’ Residue 407
NM_002971.6(SATB1):c.1588G>A (p.Glu530Lys)Pathogenic
Kohlschutter-Tonz syndrome-like|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 530
NM_002971.6(SATB1):c.211+2T>CLikely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025
NM_002971.6(SATB1):c.1848_1854del (p.Gln616fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 616
NM_002971.6(SATB1):c.1574A>G (p.Gln525Arg)Pathogenic
Kohlschutter-Tonz syndrome-like
β˜…β˜†β˜†β˜†2025β†’ Residue 525
NM_002971.6(SATB1):c.1588G>C (p.Glu530Gln)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 530
NM_002971.6(SATB1):c.1827_1830del (p.Pro610fs)Likely pathogenic
Developmental delay with dysmorphic facies and dental anomalies
β˜…β˜†β˜†β˜†2025β†’ Residue 610
NM_002971.6(SATB1):c.1633del (p.Leu545fs)Pathogenic
Developmental delay with dysmorphic facies and dental anomalies
β˜…β˜†β˜†β˜†2024β†’ Residue 545
NM_002971.6(SATB1):c.1597C>T (p.Arg533Cys)Likely pathogenic
Developmental delay with dysmorphic facies and dental anomalies
β˜…β˜†β˜†β˜†2024β†’ Residue 533
NM_002971.6(SATB1):c.1353C>A (p.Ser451Arg)Likely pathogenic
SATB1-related disorder
β˜…β˜†β˜†β˜†2024β†’ Residue 451
NM_002971.6(SATB1):c.1237dup (p.Glu413fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2024β†’ Residue 413
NM_002971.6(SATB1):c.1896dup (p.Ser633fs)Likely pathogenic
Developmental delay with dysmorphic facies and dental anomalies
β˜…β˜†β˜†β˜†2023β†’ Residue 633
NM_002971.6(SATB1):c.137_156del (p.Gly46fs)Pathogenic
Developmental delay with dysmorphic facies and dental anomalies
β˜…β˜†β˜†β˜†2023β†’ Residue 46
NM_002971.6(SATB1):c.962del (p.Leu321fs)Pathogenic
Developmental delay with dysmorphic facies and dental anomalies
β˜…β˜†β˜†β˜†2023β†’ Residue 321
NM_002971.6(SATB1):c.1522C>T (p.Arg508Cys)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 508
NM_002971.6(SATB1):c.2137G>T (p.Glu713Ter)Likely pathogenic
Kohlschutter-Tonz syndrome-like
β˜…β˜†β˜†β˜†2023β†’ Residue 713
NM_002971.6(SATB1):c.1204C>G (p.Gln402Glu)Likely pathogenic
Developmental delay with dysmorphic facies and dental anomalies
β˜…β˜†β˜†β˜†2023β†’ Residue 402
View on ClinVar β†—
Related Genes
GATAD1Shared pathway100%PIAS1Protein interaction100%CASP6Protein interaction87%HDAC1Protein interaction86%SATB2Protein interaction74%FOXP1Protein interaction73%
Tissue Expression6 tissues
Bone Marrow
100%
Heart
95%
Brain
72%
Lung
37%
Liver
33%
Ovary
27%
Gene Interaction Network
Click a node to explore
SATB1GATAD1PIAS1CASP6HDAC1SATB2FOXP1
PROTEIN STRUCTURE
Preparing viewer…
PDB3NZL Β· 1.20 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.21Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.12 [0.07–0.21]
RankingsWhere SATB1 stands among ~20K protein-coding genes
  • #1,747of 20,598
    Most Researched231 Β· top 10%
  • #1,667of 5,498
    Most Pathogenic Variants35
  • #502of 17,882
    Most Constrained (LOEUF)0.21 Β· top 5%
Genes detectedSATB1
Sources retrieved27 papers
Response timeβ€”
πŸ“„ Sources
27β–Ό
1
The role of transcription factors in shaping regulatory T cell identity.
PMID: 37336954
Nat Rev Immunol Β· 2023
1.00
2
Thymus and autoimmunity.
PMID: 33537838
Semin Immunopathol Β· 2021
0.90
3
Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction.
PMID: 33513338
Am J Hum Genet Β· 2021
0.80
4
SATB1, senescence and senescence-related diseases.
PMID: 38801120
J Cell Physiol Β· 2024
0.76
5
TGF-Ξ²-mediated silencing of genomic organizer SATB1 promotes Tfh cell differentiation and formation of intra-tumoral tertiary lymphoid structures.
PMID: 35021053
Immunity Β· 2022
0.70