NR2F2
nuclear receptor subfamily 2 group F member 2, the group of Nuclear receptor subfamily 2 group F|MicroRNA protein coding host genes
Basic information
Region (hg38): 15:96325938-96340263
Previous symbols: [ "ARP1", "TFCOUP2" ]
Links
Phenotypes
GenCC
Source:
- congenital heart defects, multiple types, 4 (Moderate), mode of inheritance: AD
- congenital heart defects, multiple types, 4 (Strong), mode of inheritance: AD
- NR2F2 related multiple congenital anomalies/dysmorphic syndrome (Definitive), mode of inheritance: AD
- 46,xx sex reversal 5 (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Congenital heart defects, multiple types, 4; 46 XX sex reversal 5 | AD | Cardiovascular | The conditions can involve congenital cardiac anomalies, and awareness may allow early management | Cardiovascular; Craniofacial; Endocrine; Genitourinary; Ophthalmologic | 18371933; 24702954; 29478779; 31687637 |
ClinVar
This is a list of variants' phenotypes submitted to
- Congenital_heart_defects,_multiple_types,_4 (75 variants)
- not_provided (32 variants)
- Inborn_genetic_diseases (23 variants)
- NR2F2_associated_disorders (7 variants)
- NR2F2-related_disorder (6 variants)
- 46,xx_sex_reversal_5 (4 variants)
- not_specified (3 variants)
- Neurodevelopmental_disorder (1 variants)
- NR2F2-Releated_Disorders (1 variants)
- NR2F2-related_congenital_heart_defects (1 variants)
- 46,XY_disorder_of_sex_development (1 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
- Congenital_heart_disease_(variable) (1 variants)
- Asplenia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR2F2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021005.4. 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 | 34 | 35 | ||||
| missense | 67 | 78 | ||||
| nonsense | 12 | |||||
| start loss | 0 | |||||
| frameshift | 13 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 18 | 17 | 68 | 36 | 1 |
Highest pathogenic variant AF is 6.1957945e-7
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NR2F2 | protein_coding | protein_coding | ENST00000394166 | 3 | 14326 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.990 | 0.0103 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.60 | 79 | 234 | 0.338 | 0.0000126 | 2705 |
| Missense in Polyphen | 15 | 105.28 | 0.14248 | 1142 | ||
| Synonymous | -2.38 | 132 | 101 | 1.30 | 0.00000591 | 838 |
| Loss of Function | 3.44 | 0 | 13.8 | 0.00 | 5.95e-7 | 155 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ligand-activated transcription factor. Activated by high concentrations of 9-cis-retinoic acid and all-trans-retinoic acid, but not by dexamethasone, cortisol or progesterone (in vitro). Regulation of the apolipoprotein A-I gene transcription. Binds to DNA site A. {ECO:0000269|PubMed:18798693, ECO:0000269|PubMed:1899293, ECO:0000269|PubMed:9343308}.;
- Pathway
- NHR;Nuclear Receptors;White fat cell differentiation;Ectoderm Differentiation;White fat cell differentiation;FOXA1 transcription factor network;Regulation of Telomerase
(Consensus)
Recessive Scores
- pRec
- 0.292
Intolerance Scores
- loftool
- rvis_EVS
- -0.41
- rvis_percentile_EVS
- 26.23
Haploinsufficiency Scores
- pHI
- 0.871
- hipred
- Y
- hipred_score
- 0.717
- ghis
- 0.623
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.944
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nr2f2
- Phenotype
- immune system 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); digestive/alimentary phenotype; vision/eye phenotype; reproductive system 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); pigmentation phenotype; embryo phenotype; homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- nr2f2
- Affected structure
- thoracic duct
- Phenotype tag
- abnormal
- Phenotype quality
- immature
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;neuron migration;maternal placenta development;negative regulation of endothelial cell proliferation;positive regulation of systemic arterial blood pressure;regulation of transcription by RNA polymerase II;lipid metabolic process;signal transduction;skeletal muscle tissue development;fertilization;anterior/posterior pattern specification;radial pattern formation;negative regulation of endothelial cell migration;intracellular receptor signaling pathway;forebrain development;response to estradiol;steroid hormone mediated signaling pathway;negative regulation of cyclin-dependent protein serine/threonine kinase activity;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;blood vessel morphogenesis;limb development;placenta blood vessel development;trophoblast giant cell differentiation;regulation of transcription involved in lymphatic endothelial cell fate commitment
- Cellular component
- nucleus;nucleoplasm;cytosol
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;retinoic acid binding;DNA-binding transcription factor activity;steroid hormone receptor activity;transcription corepressor activity;nuclear receptor activity;protein binding;zinc ion binding;protein homodimerization activity;sequence-specific DNA binding