NR5A2
nuclear receptor subfamily 5 group A member 2, the group of Nuclear receptor subfamily 5 group A
Basic information
Region (hg38): 1:200027614-200177420
Previous symbols: [ "FTF" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (48 variants)
- not_provided (3 variants)
- Premature_ovarian_failure (1 variants)
- Anophthalmia-microphthalmia_syndrome (1 variants)
- Long_QT_syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR5A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000205860.3. 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 | 2 | |||||
| missense | 46 | 50 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 46 | 4 | 1 |
Highest pathogenic variant AF is 0.00000991266
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NR5A2 | protein_coding | protein_coding | ENST00000367362 | 8 | 149823 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.238 | 0.762 | 125716 | 0 | 32 | 125748 | 0.000127 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.38 | 222 | 288 | 0.771 | 0.0000148 | 3556 |
| Missense in Polyphen | 22 | 64.922 | 0.33887 | 790 | ||
| Synonymous | -0.601 | 117 | 109 | 1.07 | 0.00000577 | 1020 |
| Loss of Function | 3.82 | 7 | 29.3 | 0.239 | 0.00000181 | 298 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000506 | 0.000489 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000561 | 0.000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000107 | 0.000105 |
| Middle Eastern | 0.000561 | 0.000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000166 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Nuclear receptor that acts as a key metabolic sensor by regulating the expression of genes involved in bile acid synthesis, cholesterol homeostasis and triglyceride synthesis. Together with the oxysterol receptors NR1H3/LXR-alpha and NR1H2/LXR-beta, acts as an essential transcriptional regulator of lipid metabolism. Plays an anti-inflammatory role during the hepatic acute phase response by acting as a corepressor: inhibits the hepatic acute phase response by preventing dissociation of the N-Cor corepressor complex (PubMed:20159957). Binds to the sequence element 5'-AACGACCGACCTTGAG-3' of the enhancer II of hepatitis B virus genes, a critical cis-element of their expression and regulation. May be responsible for the liver-specific activity of enhancer II, probably in combination with other hepatocyte transcription factors. Key regulator of cholesterol 7-alpha- hydroxylase gene (CYP7A) expression in liver. May also contribute to the regulation of pancreas-specific genes and play important roles in embryonic development. {ECO:0000269|PubMed:15707893, ECO:0000269|PubMed:15723037, ECO:0000269|PubMed:15897460, ECO:0000269|PubMed:16289203, ECO:0000269|PubMed:20159957}.;
- Pathway
- Maturity onset diabetes of the young - Homo sapiens (human);NHR;Nuclear Receptors;Steatosis AOP;Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription
(Consensus)
Recessive Scores
- pRec
- 0.405
Intolerance Scores
- loftool
- 0.0846
- rvis_EVS
- -0.29
- rvis_percentile_EVS
- 33.2
Haploinsufficiency Scores
- pHI
- 0.922
- hipred
- Y
- hipred_score
- 0.875
- ghis
- 0.440
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.962
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nr5a2
- Phenotype
- embryo phenotype; liver/biliary system phenotype; 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); 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; digestive/alimentary phenotype; immune system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- nr5a2
- Affected structure
- cranial cartilage
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;transcription initiation from RNA polymerase II promoter;bile acid metabolic process;hormone-mediated signaling pathway;embryo development ending in birth or egg hatching;tissue development;intracellular receptor signaling pathway;epithelial cell differentiation;regulation of cell population proliferation;homeostatic process;cholesterol homeostasis;steroid hormone mediated signaling pathway;positive regulation of viral genome replication;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;pancreas morphogenesis;calcineurin-mediated signaling;cellular response to leukemia inhibitory factor
- Cellular component
- nucleus;nucleoplasm;cytoplasm;RNA polymerase II transcription factor complex
- Molecular function
- transcription regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;chromatin binding;DNA-binding transcription factor activity;steroid hormone receptor activity;nuclear receptor activity;protein binding;phospholipid binding;zinc ion binding;sequence-specific DNA binding;transcription regulatory region DNA binding