SATB2
SATB homeobox 2, the group of CUT class homeoboxes and pseudogenes
Basic information
Region (hg38): 2:199269505-199471266
Links
Phenotypes
GenCC
Source:
- chromosome 2q32-q33 deletion syndrome (Definitive), mode of inheritance: AD
- chromosome 2q32-q33 deletion syndrome (Moderate), mode of inheritance: AD
- SATB2 associated disorder (Definitive), mode of inheritance: AD
- chromosome 2q32-q33 deletion syndrome (Strong), mode of inheritance: AD
- SATB2 associated disorder (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Glass syndrome | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Dental; Musculoskeletal; Neurologic | 17377962; 19170718; 19668335; 22521361; 23925499; 24301056; 24363063; 25118029 |
ClinVar
This is a list of variants' phenotypes submitted to
- Chromosome_2q32-q33_deletion_syndrome (662 variants)
- not_provided (184 variants)
- Inborn_genetic_diseases (100 variants)
- SATB2-related_disorder (38 variants)
- not_specified (11 variants)
- Intellectual_disability (10 variants)
- SATB2_associated_disorder (8 variants)
- Global_developmental_delay (3 variants)
- Neurodevelopmental_disorder (2 variants)
- See_cases (2 variants)
- Cleft_palate (2 variants)
- Isolated_cleft_palate (1 variants)
- SATB2-associated_syndrome (1 variants)
- intellectual_deficiency (1 variants)
- Autism_spectrum_disorder (1 variants)
- Hyperplasia_of_midface (1 variants)
- Abnormality_of_the_dentition (1 variants)
- Microcephaly (1 variants)
- Speech_articulation_difficulties (1 variants)
- Clinodactyly_of_the_5th_finger (1 variants)
- Neurodevelopmental_abnormality (1 variants)
- Dolichocephaly (1 variants)
- Micrognathia (1 variants)
- Dystonic_disorder (1 variants)
- Cerebellar_ataxia (1 variants)
- Abnormal_facial_shape (1 variants)
- Downturned_corners_of_mouth (1 variants)
- Macrocephaly (1 variants)
- Developmental_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SATB2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001172509.2. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 210 | 216 | ||||
| missense | 16 | 36 | 203 | 48 | 42 | 345 |
| nonsense | 35 | 13 | 51 | |||
| start loss | 1 | 1 | ||||
| frameshift | 57 | 15 | 76 | |||
| splice donor/acceptor (+/-2bp) | 10 | 20 | ||||
| Total | 118 | 74 | 212 | 258 | 47 |
Highest pathogenic variant AF is 0.00000657298
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SATB2 | protein_coding | protein_coding | ENST00000417098 | 10 | 201767 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000809 | 125389 | 0 | 1 | 125390 | 0.00000399 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.05 | 183 | 415 | 0.441 | 0.0000247 | 4816 |
| Missense in Polyphen | 26 | 152.54 | 0.17044 | 1846 | ||
| Synonymous | -1.02 | 188 | 171 | 1.10 | 0.0000114 | 1436 |
| Loss of Function | 5.32 | 0 | 32.9 | 0.00 | 0.00000179 | 357 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000883 | 0.00000883 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- 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) 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. {ECO:0000269|PubMed:14701874}.;
- Disease
- DISEASE: Note=Chromosomal aberrations involving SATB2 are found in isolated cleft palate. Translocation t(2;7); translocation t(2;11). {ECO:0000269|PubMed:12915443}.; DISEASE: Cleft palate isolated (CPI) [MIM:119540]: A congenital fissure of the soft and/or hard palate, due to faulty fusion. Isolated cleft palate is not associated with cleft lips. Some patients may manifest other craniofacial dysmorphic features, mental retardation, and osteoporosis. {ECO:0000269|PubMed:12915443, ECO:0000269|PubMed:17377962}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; DISEASE: Note=A chromosomal aberration involving SATB2 is found in a patient with classical features of Toriello-Carey syndrome. Translocation t(2;14)(q33;q22). {ECO:0000269|PubMed:19170718}.;
- Pathway
- RUNX2 regulates osteoblast differentiation;RUNX2 regulates bone development;Transcriptional regulation by RUNX2;Gene expression (Transcription);Generic Transcription Pathway;SUMOylation of chromatin organization proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;RNA Polymerase II Transcription;SUMOylation
(Consensus)
Intolerance Scores
- loftool
- 0.0340
- rvis_EVS
- -0.87
- rvis_percentile_EVS
- 10.65
Haploinsufficiency Scores
- pHI
- 0.908
- hipred
- Y
- hipred_score
- 0.806
- ghis
- 0.489
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.919
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Satb2
- Phenotype
- respiratory system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; digestive/alimentary phenotype; skeleton phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- satb2
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- dead
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;neuron migration;osteoblast development;chromatin remodeling;embryonic pattern specification;commitment of neuronal cell to specific neuron type in forebrain;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis;cartilage development;roof of mouth development;cellular response to organic substance
- Cellular component
- histone deacetylase complex;nucleus;nucleoplasm;transcription factor complex;nuclear matrix
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;protein binding;sequence-specific DNA binding