EMX2
empty spiracles homeobox 2, the group of NKL subclass homeoboxes and pseudogenes
Basic information
Region (hg38): 10:117542445-117549546
Links
Phenotypes
GenCC
Source:
- schizencephaly (Limited), mode of inheritance: AD
- schizencephaly (Moderate), mode of inheritance: AD
- schizencephaly (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Schizencephaly | 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 | Neurologic | 8528262; 9359037; 17506092; 18409201 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (24 variants)
- not_provided (13 variants)
- Schizencephaly (9 variants)
- Congenital_hypogonadotropic_hypogonadism (8 variants)
- not_specified (5 variants)
- EMX2-related_disorder (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMX2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004098.4. 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 | 11 | |||||
| missense | 25 | 32 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 4 | 1 | 27 | 13 | 1 |
Highest pathogenic variant AF is 6.84162e-7
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EMX2 | protein_coding | protein_coding | ENST00000553456 | 3 | 7102 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.951 | 0.0492 | 113689 | 0 | 1 | 113690 | 0.00000440 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.57 | 94 | 148 | 0.637 | 0.00000676 | 1608 |
| Missense in Polyphen | 18 | 41.449 | 0.43427 | 486 | ||
| Synonymous | 0.503 | 63 | 68.3 | 0.923 | 0.00000342 | 523 |
| Loss of Function | 2.85 | 0 | 9.47 | 0.00 | 4.33e-7 | 96 |
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) | 0.0000214 | 0.0000101 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor, which in cooperation with EMX2, acts to generate the boundary between the roof and archipallium in the developing brain. May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.;
Recessive Scores
- pRec
- 0.315
Intolerance Scores
- loftool
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.938
- hipred
- Y
- hipred_score
- 0.837
- ghis
- 0.537
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.772
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Emx2
- Phenotype
- renal/urinary system phenotype; skeleton phenotype; vision/eye phenotype; hearing/vestibular/ear 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); 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; cellular phenotype; craniofacial phenotype; taste/olfaction phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- emx2
- Affected structure
- neuromast hair cell
- Phenotype tag
- abnormal
- Phenotype quality
- orientation
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;anterior/posterior pattern specification;dentate gyrus development;cerebral cortex regionalization;cell proliferation in forebrain;forebrain cell migration;neuron differentiation;response to drug;renal system development
- Cellular component
- nucleus
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding