Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
23314
Gene name Gene Name - the full gene name approved by the HGNC.
SATB homeobox 2
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
SATB2
Synonyms (NCBI Gene) Gene synonyms aliases
C2DELq32q33, DEL2Q32Q33, GLSS
Chromosome Chromosome number
2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
2q33.1
Summary Summary of gene provided in NCBI Entrez Gene.
This gene encodes a DNA binding protein that specifically binds nuclear matrix attachment regions. The encoded protein is involved in transcription regulation and chromatin remodeling. Defects in this gene are associated with isolated cleft palate and cog
SNPs SNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs137853127 G>A Pathogenic Stop gained, coding sequence variant, genic downstream transcript variant
rs797044874 G>A Pathogenic Coding sequence variant, stop gained, genic downstream transcript variant
rs863224917 G>A Likely-pathogenic Coding sequence variant, missense variant, genic downstream transcript variant
rs875989830 AC>- Pathogenic Frameshift variant, coding sequence variant, genic downstream transcript variant
rs878853163 T>A,C Pathogenic Coding sequence variant, stop gained, missense variant, genic downstream transcript variant
miRNA miRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT006567 hsa-miR-31-5p Luciferase reporter assay 20980827
MIRT006567 hsa-miR-31-5p Luciferase reporter assay 20980827
MIRT025532 hsa-miR-34a-5p Sequencing 20371350
MIRT026761 hsa-miR-192-5p Microarray 19074876
MIRT045505 hsa-miR-149-5p CLASH 23622248
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0000118 Component Histone deacetylase complex IEA
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
GO:0000785 Component Chromatin ISA
GO:0000977 Function RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA 22825848
GO:0000977 Function RNA polymerase II transcription regulatory region sequence-specific DNA binding IEA
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
608148 21637 ENSG00000119042
Protein
UniProt ID Q9UPW6
Protein name DNA-binding protein SATB2 (Special AT-rich sequence-binding protein 2)
Protein function 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)
PDB 1WI3 , 1WIZ , 2CSF
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF16534 ULD 58 156 Ubiquitin-like oligomerisation domain of SATB Domain
PF16557 CUTL 162 233 CUT1-like DNA-binding domain of SATB Domain
PF02376 CUT 355 434 CUT domain Domain
PF02376 CUT 478 557 CUT domain Domain
PF00046 Homeodomain 615 672 Homeodomain Domain
Tissue specificity TISSUE SPECIFICITY: High expression in adult brain, moderate expression in fetal brain, and weak expression in adult liver, kidney, and spinal cord and in select brain regions, including amygdala, corpus callosum, caudate nucleus, and hippocampus. {ECO:00
Sequence
MERRSESPCLRDSPDRRSGSPDVKGPPPVKVARLEQNGSPMGARGRPNGAVAKAVGGLMI
PVFCVVEQLDGSLEYDNREEHAEFVLVRKDVLFSQLVETALLALGYSHSSAAQAQGIIKL
GRWNPLPLSYVTDAPDATVADMLQDVYHVVTLKIQL
QSCSKLEDLPAEQWNHATVRNALK
ELLKEMNQSTLAKECPLSQSMISSIVNSTYYANVSATKCQEFGRWYKKYKKIK
VERVERE
NLSDYCVLGQRPMHLPNMNQLASLGKTNEQSPHSQIHHSTPIRNQVPALQPIMSPGLLSP
QLSPQLVRQQIAMAHLINQQIAVSRLLAHQHPQAINQQFLNHPPIPRAVKPEPTNSSVEV
SPDIYQQVRDELKRASVSQAVFARVAFNRTQGLLSEILRKEEDPRTASQSLLVNLRAMQN
FLNLPEVERDRIYQ
DERERSMNPNVSMVSSASSSPSSSRTPQAKTSTPTTDLPIKVDGAN
INITAAIYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLCT
IRRFLNLPQHERDVIYE
EESRHHHSERMQHVVQLPPEPVQVLHRQQSQPAKESSPPREEA
PPPPPPTEDSCAKKPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTII
KFFQNQRYHVKH
HGKLKEHLGSAVDVAEYKDEELLTESEENDSEEGSEEMYKVEAEEENA
DKSKAAPAEIDQR
Sequence length 733
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    SUMOylation of chromatin organization proteins
<
Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
2q32-q33 Deletion Syndrome chromosome 2q32-q33 deletion syndrome rs1574492395, rs2105928778, rs1553547838, rs1574532452, rs875989830, rs1553544187, rs1574566973, rs878853163, rs1559052032, rs1574532220, rs886041847, rs1559016679, rs1574566833, rs886041516, rs1357010510
View all (16 more)
N/A
satb2 associated disorder SATB2 associated disorder rs797044874 N/A
Mental retardation intellectual disability rs1574554519, rs1574511051, rs137853127 N/A
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Colorectal Cancer Colorectal cancer N/A N/A GWAS
Dyslexia Dyslexia N/A N/A GWAS
Schizophrenia Schizophrenia N/A N/A GWAS
Ulcerative colitis Ulcerative colitis N/A N/A GWAS
Associations from Text Mining Disease associations identified through Pubtator
Disease Name Relationship Type References
Achard syndrome Associate 21343628
Adenocarcinoma Mucinous Associate 30962505, 36351995
Adenocarcinoma of Lung Associate 34550610, 37107669, 37349623
Adenoma Associate 35917493
Adenomyoma Associate 33459390
Anodontia Associate 25118029
Aphasia Conduction Associate 25118029, 27409069, 34241948, 40225157, 40474278
Appendiceal Neoplasms Associate 31233624
Arthritis Juvenile Associate 30013183
Ascending aortic aneurysm hypertelorism bifid uvula cleft palate and arterial tortuosity Associate 40474278