SATB1
SATB homeobox 1, the group of CUT class homeoboxes and pseudogenes
Basic information
Region (hg38): 3:18345377-18445621
Links
Phenotypes
GenCC
Source:
- syndromic intellectual disability (Supportive), mode of inheritance: AD
- developmental delay with dysmorphic facies and dental anomalies (Strong), mode of inheritance: AD
- complex neurodevelopmental disorder (Definitive), mode of inheritance: AD
- neurodevelopmental disorder (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Developmental delay with dysmorphic facies and dental anomalies; den Hoed-de Boer-Voisin syndrome (Kohlschutter-Tonz syndrome-like) | AD | Cardiovascular | The conditions can involve congenital cardiac anomalies, and awareness may allow early management | Cardiovascular; Craniofacial; Dental; Musculoskeletal; Neurologic; Ophthalmologic | 33513338 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (91 variants)
- Inborn_genetic_diseases (45 variants)
- Developmental_delay_with_dysmorphic_facies_and_dental_anomalies (31 variants)
- SATB1-related_disorder (15 variants)
- Kohlschutter-Tonz_syndrome-like (15 variants)
- not_specified (8 variants)
- Neurodevelopmental_disorder (2 variants)
- Autism_spectrum_disorder (1 variants)
- Neurodevelopmental_delay (1 variants)
- SATB1-related_neurodevelopmental_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SATB1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002971.6. 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 | 10 | 13 | ||||
| missense | 10 | 100 | 121 | |||
| nonsense | 9 | |||||
| start loss | 0 | |||||
| frameshift | 10 | 22 | ||||
| splice donor/acceptor (+/-2bp) | 3 | |||||
| Total | 17 | 18 | 115 | 16 | 2 |
Highest pathogenic variant AF is 0.000006574449
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SATB1 | protein_coding | protein_coding | ENST00000417717 | 11 | 100202 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.991 | 0.00949 | 125742 | 0 | 6 | 125748 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.98 | 202 | 436 | 0.463 | 0.0000247 | 5204 |
| Missense in Polyphen | 49 | 156.49 | 0.31312 | 1864 | ||
| Synonymous | -1.07 | 192 | 174 | 1.10 | 0.0000109 | 1550 |
| Loss of Function | 5.02 | 6 | 40.4 | 0.148 | 0.00000222 | 431 |
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 | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000382 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Crucial silencing factor contributing to the initiation of X inactivation mediated by Xist RNA that occurs during embryogenesis and in lymphoma (By similarity). Binds to DNA at special AT-rich sequences, the consensus SATB1-binding sequence (CSBS), at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double-stranded DNA. Transcriptional repressor controlling nuclear and viral gene expression in a phosphorylated and acetylated status-dependent manner, 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 (e.g. PML at the MHC-I locus) and also by recruiting corepressors (HDACs) or coactivators (HATs) directly to promoters and enhancers. Modulates genes that are essential in the maturation of the immune T-cell CD8SP from thymocytes. Required for the switching of fetal globin species, and beta- and gamma-globin genes regulation during erythroid differentiation. Plays a role in chromatin organization and nuclear architecture during apoptosis. Interacts with the unique region (UR) of cytomegalovirus (CMV). Alu-like motifs and SATB1- binding sites provide a unique chromatin context which seems preferentially targeted by the HIV-1 integration machinery. Moreover, HIV-1 Tat may overcome SATB1-mediated repression of IL2 and IL2RA (interleukin) in T-cells by binding to the same domain than HDAC1. Delineates specific epigenetic modifications at target gene loci, directly up-regulating metastasis-associated genes while down-regulating tumor-suppressor genes. Reprograms chromatin organization and the transcription profiles of breast tumors to promote growth and metastasis. {ECO:0000250, ECO:0000269|PubMed:10595394, ECO:0000269|PubMed:11463840, ECO:0000269|PubMed:12374985, ECO:0000269|PubMed:12692553, ECO:0000269|PubMed:1505028, ECO:0000269|PubMed:15618465, ECO:0000269|PubMed:15713622, ECO:0000269|PubMed:16377216, ECO:0000269|PubMed:16630892, ECO:0000269|PubMed:17173041, ECO:0000269|PubMed:17376900, ECO:0000269|PubMed:18337816, ECO:0000269|PubMed:19103759, ECO:0000269|PubMed:19247486, ECO:0000269|PubMed:19332023, ECO:0000269|PubMed:19430959, ECO:0000269|PubMed:9111059, ECO:0000269|PubMed:9548713}.;
- Pathway
- Vitamin D Receptor Pathway;SUMOylation of chromatin organization proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;Apoptotic cleavage of cellular proteins;Apoptotic execution phase;Apoptosis;Programmed Cell Death;SUMOylation;Caspase Cascade in Apoptosis
(Consensus)
Recessive Scores
- pRec
- 0.158
Intolerance Scores
- loftool
- 0.363
- rvis_EVS
- -0.58
- rvis_percentile_EVS
- 18.59
Haploinsufficiency Scores
- pHI
- 0.155
- hipred
- Y
- hipred_score
- 0.651
- ghis
- 0.541
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.896
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Satb1
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; limbs/digits/tail phenotype; 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); vision/eye 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); hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- satb1b
- Affected structure
- thrombocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;chromatin organization;chromatin remodeling;epidermis development;viral process;histone methylation;CD4-positive, alpha-beta T cell differentiation;CD8-positive, alpha-beta T cell differentiation;activated T cell proliferation;reflex
- Cellular component
- nucleus;nucleoplasm;nuclear heterochromatin;nuclear matrix;nuclear body;PML body
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;chromatin binding;double-stranded DNA binding;protein binding;sequence-specific DNA binding