NR4A1
nuclear receptor subfamily 4 group A member 1, the group of Nuclear receptor subfamily 4 group A
Basic information
Region (hg38): 12:52022832-52059507
Previous symbols: [ "HMR", "GFRP1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (53 variants)
- not_provided (10 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR4A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173157.3. 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 | 7 | |||||
| missense | 53 | 54 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 53 | 4 | 4 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NR4A1 | protein_coding | protein_coding | ENST00000360284 | 7 | 36676 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.371 | 0.629 | 125728 | 0 | 17 | 125745 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.51 | 289 | 371 | 0.779 | 0.0000230 | 3872 |
| Missense in Polyphen | 113 | 171.48 | 0.65897 | 1862 | ||
| Synonymous | 0.179 | 166 | 169 | 0.982 | 0.0000110 | 1325 |
| Loss of Function | 3.38 | 5 | 22.2 | 0.225 | 0.00000112 | 252 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000655 | 0.0000615 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000807 | 0.0000791 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000170 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Orphan nuclear receptor. May act concomitantly with NURR1 in regulating the expression of delayed-early genes during liver regeneration. Binds the NGFI-B response element (NBRE) 5'- AAAAGGTCA-3' (By similarity). May inhibit NF-kappa-B transactivation of IL2. Participates in energy homeostasis by sequestrating the kinase STK11 in the nucleus, thereby attenuating cytoplasmic AMPK activation. Plays a role in the vascular response to injury (By similarity). {ECO:0000250, ECO:0000250|UniProtKB:P12813, ECO:0000269|PubMed:15466594, ECO:0000269|PubMed:22983157}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Cortisol synthesis and secretion - Homo sapiens (human);Aldosterone synthesis and secretion - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);NHR;Nuclear Receptors;Corticotropin-releasing hormone signaling pathway;Spinal Cord Injury;MAPK Signaling Pathway;VEGFA-VEGFR2 Signaling Pathway;HDAC6 interactions;Disease;Signal Transduction;Gene expression (Transcription);role of mef2d in t-cell apoptosis;Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription;AKT phosphorylates targets in the nucleus;Glucocorticoid receptor regulatory network;PIP3 activates AKT signaling;RXR and RAR heterodimerization with other nuclear receptor;Constitutive Signaling by AKT1 E17K in Cancer;PI3K/AKT Signaling in Cancer;Intracellular signaling by second messengers;Diseases of signal transduction;Role of Calcineurin-dependent NFAT signaling in lymphocytes
(Consensus)
Recessive Scores
- pRec
- 0.624
Intolerance Scores
- loftool
- 0.0558
- rvis_EVS
- -1.24
- rvis_percentile_EVS
- 5.41
Haploinsufficiency Scores
- pHI
- 0.293
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.602
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nr4a1
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region 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); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; neoplasm; 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); hematopoietic system phenotype; normal 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;
Gene ontology
- Biological process
- positive regulation of endothelial cell proliferation;cell migration involved in sprouting angiogenesis;transcription initiation from RNA polymerase II promoter;signal transduction;intracellular receptor signaling pathway;endothelial cell chemotaxis;cellular response to vascular endothelial growth factor stimulus;steroid hormone mediated signaling pathway;cellular response to fibroblast growth factor stimulus;fat cell differentiation;negative regulation of cell cycle;positive regulation of transcription by RNA polymerase II;regulation of type B pancreatic cell proliferation;cellular response to corticotropin-releasing hormone stimulus
- Cellular component
- nucleus;nucleoplasm;transcription factor complex;cytosol;nuclear membrane
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;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;DNA binding;steroid hormone receptor activity;nuclear receptor activity;protein binding;zinc ion binding;glucocorticoid receptor binding;sequence-specific DNA binding;protein heterodimerization activity