ZEB2
zinc finger E-box binding homeobox 2, the group of ZF class homeoboxes and pseudogenes|Zinc fingers C2H2-type
Basic information
Region (hg38): 2:144364364-144521057
Previous symbols: [ "ZFHX1B" ]
Links
Phenotypes
GenCC
Source:
- Mowat-Wilson syndrome (Definitive), mode of inheritance: AD
- Mowat-Wilson syndrome (Strong), mode of inheritance: AD
- Mowat-Wilson syndrome (Definitive), mode of inheritance: AD
- Mowat-Wilson syndrome (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Mowat-Wilson syndrome | AD | General | The condition can include Hirschsprung disease, among other multi-systemic manifestations; 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; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic | 9719364; 11448942; 11279515; 14679597; 15121779; 16088920; 16688751; 16532472; 17203459; 19215041;20301585; 21343952; 21497296; 22246645; 22486326; 23322667; 23427518; 23466526; 23523603; 24029077; 24715670; 27831545 |
ClinVar
This is a list of variants' phenotypes submitted to
- Mowat-Wilson_syndrome (1186 variants)
- not_provided (360 variants)
- Inborn_genetic_diseases (176 variants)
- not_specified (140 variants)
- ZEB2-related_disorder (50 variants)
- See_cases (4 variants)
- Neurodevelopmental_disorder (3 variants)
- Intellectual_disability (3 variants)
- Marfanoid_habitus_and_intellectual_disability (2 variants)
- Cleft_lip/palate (1 variants)
- Hirschsprung_disease-intellectual_disability_syndrome,_late_infantile (1 variants)
- Neurodevelopmental_delay (1 variants)
- Lennox-Gastaut_syndrome (1 variants)
- Abnormal_brain_morphology (1 variants)
- Abnormality_of_the_nervous_system (1 variants)
- Fetal_akinesia_deformation_sequence_1 (1 variants)
- Megacolon (1 variants)
- Aganglionic_megacolon (1 variants)
- Smith-Magenis_Syndrome-like (1 variants)
- Megalencephaly-polymicrogyria-polydactyly-hydrocephalus_syndrome_1 (1 variants)
- Arthrogryposis_multiplex_congenita (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZEB2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014795.4. 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 | 303 | 315 | ||||
| missense | 17 | 26 | 438 | 158 | 43 | 682 |
| nonsense | 91 | 13 | 106 | |||
| start loss | 2 | 2 | ||||
| frameshift | 195 | 25 | 224 | |||
| splice donor/acceptor (+/-2bp) | 12 | 20 | ||||
| Total | 315 | 71 | 454 | 461 | 48 |
Highest pathogenic variant AF is 0.0000020521632
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ZEB2 | protein_coding | protein_coding | ENST00000558170 | 9 | 140500 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 5.99e-7 | 124846 | 0 | 1 | 124847 | 0.00000400 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.94 | 378 | 664 | 0.569 | 0.0000377 | 8112 |
| Missense in Polyphen | 73 | 211.53 | 0.34511 | 2608 | ||
| Synonymous | -0.233 | 264 | 259 | 1.02 | 0.0000165 | 2239 |
| Loss of Function | 6.03 | 1 | 44.3 | 0.0226 | 0.00000251 | 583 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000993 | 0.0000993 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional inhibitor that binds to DNA sequence 5'- CACCT-3' in different promoters. Represses transcription of E- cadherin. {ECO:0000269|PubMed:16061479}.;
- Disease
- DISEASE: Mowat-Wilson syndrome (MOWS) [MIM:235730]: A complex developmental disorder characterized by mental retardation, delayed motor development, epilepsy, microcephaly and a wide spectrum of clinically heterogeneous features suggestive of neurocristopathies at the cephalic, cardiac, and vagal levels. Affected patients show an easily recognizable facial appearance with deep set eyes and hypertelorism, medially divergent, broad eyebrows, prominent columella, pointed chin and uplifted, notched ear lobes. Some patients manifest Hirschsprung disease. {ECO:0000269|PubMed:11448942, ECO:0000269|PubMed:12451214, ECO:0000269|PubMed:15384097, ECO:0000269|PubMed:16688751}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- MicroRNAs in cancer - Homo sapiens (human);TGF-beta Signaling Pathway;EMT transition in Colorectal Cancer;TGF-beta Receptor Signaling;TGF_beta_Receptor
(Consensus)
Recessive Scores
- pRec
- 0.223
Intolerance Scores
- loftool
- 0.0187
- rvis_EVS
- -0.91
- rvis_percentile_EVS
- 10.03
Haploinsufficiency Scores
- pHI
- 0.894
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.550
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.960
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zeb2
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; cellular 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); reproductive system phenotype; pigmentation 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;
Zebrafish Information Network
- Gene name
- zeb2b
- Affected structure
- intrahepatic bile duct
- Phenotype tag
- abnormal
- Phenotype quality
- decreased length
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;neural crest cell migration;somitogenesis;neural tube closure;nervous system development;corpus callosum morphogenesis;hippocampus development;cell proliferation in forebrain;corticospinal tract morphogenesis;positive regulation of Wnt signaling pathway;positive regulation of JUN kinase activity;positive regulation of melanocyte differentiation;positive regulation of transcription by RNA polymerase II;positive regulation of melanin biosynthetic process;developmental pigmentation;collateral sprouting;positive regulation of axonogenesis;mammillary axonal complex development;melanocyte migration;positive regulation of lens fiber cell differentiation;regulation of melanosome organization
- Cellular component
- nuclear chromatin;nucleus;nucleolus;cytosol
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding;phosphatase regulator activity;sequence-specific DNA binding;metal ion binding;R-SMAD binding