RXRA

retinoid X receptor alpha, the group of MicroRNA protein coding host genes|Retinoid X receptors

Basic information

Region (hg38): 9:134317097-134440585

Links

ENSG00000186350 ∙ NCBI:6256 ∙ OMIM:180245 ∙ HGNC:10477 ∙ Uniprot:P19793 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RXRA gene.

• Inborn genetic diseases (6 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RXRA gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in RXRA

This is a list of pathogenic ClinVar variants found in the RXRA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-134319017-T-C		Levothyroxine response	drug response (-)
9-134326660-G-A			Uncertain significance (Oct 07, 2020)
9-134401726-C-T			Likely benign (Jul 17, 2018)
9-134401735-G-A			Likely benign (May 21, 2018)
9-134409080-C-T		not specified	Uncertain significance (Jan 25, 2023)
9-134409102-T-C		not specified	Uncertain significance (Mar 07, 2023)
9-134417178-C-T		not specified	Uncertain significance (Mar 16, 2022)
9-134417195-C-A		not specified	Uncertain significance (Jan 26, 2022)
9-134417208-G-C		not specified	Uncertain significance (Feb 05, 2024)
9-134417218-G-A		Multiple myeloma	Likely pathogenic (Aug 31, 2019)
9-134417221-G-A		not specified	Uncertain significance (Jun 05, 2023)
9-134417311-G-C		not specified	Uncertain significance (Jan 03, 2024)
9-134434138-C-T		not specified	Uncertain significance (Dec 13, 2022)
9-134436505-C-A		Pancreatic adenocarcinoma • Transitional cell carcinoma of the bladder • Hepatocellular carcinoma	Likely pathogenic (May 31, 2016)
9-134436505-C-T		Transitional cell carcinoma of the bladder • Pancreatic adenocarcinoma • Hepatocellular carcinoma	Likely pathogenic (May 31, 2016)
9-134436587-G-A		not specified	Uncertain significance (Feb 13, 2024)
9-134436594-G-A		not specified	Uncertain significance (Feb 27, 2024)
9-134436595-C-T		not specified	Uncertain significance (Dec 14, 2021)
9-134436600-C-T		not specified	Uncertain significance (Feb 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RXRA	protein_coding	protein_coding	ENST00000481739	10	123488

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00148	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.97	163	310	0.526	0.0000209	3005
Missense in Polyphen		50	145.04	0.34473		1368
Synonymous	-0.291	143	139	1.03	0.0000104	937
Loss of Function	4.04	0	19.0	0.00	8.89e-7	228

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: dbNSFP

• Function: FUNCTION: Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as a common heterodimeric partner for a number of nuclear receptors. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes. {ECO:0000269|PubMed:10195690, ECO:0000269|PubMed:11162439, ECO:0000269|PubMed:11915042, ECO:0000269|PubMed:20215566}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Non-small cell lung cancer - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Adipocytokine signaling pathway - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Bile secretion - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Thyroid cancer - Homo sapiens (human);NHR;Vitamin D Metabolism;Energy Metabolism;Nuclear Receptors;Adipogenesis;Liver X Receptor Pathway;Constitutive Androstane Receptor Pathway;Pregnane X Receptor pathway;Vitamin D Receptor Pathway;PPAR Alpha Pathway;Farnesoid X Receptor Pathway;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;Transcription factor regulation in adipogenesis;Angiopoietin Like Protein 8 Regulatory Pathway;PPAR signaling pathway;Prion disease pathway;PI3K-AKT-mTOR - VitD3 Signalling;role of ppar-gamma coactivators in obesity and thermogenesis;Vitamin A and Carotenoid Metabolism;Developmental Biology;Signal Transduction;Gene expression (Transcription);mechanism of gene regulation by peroxisome proliferators via ppara;visceral fat deposits and the metabolic syndrome;Phase I - Functionalization of compounds;transcription regulation by methyltransferase of carm1;nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells;Generic Transcription Pathway;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;Regulation of pyruvate dehydrogenase (PDH) complex;Pyruvate metabolism;basic mechanism of action of ppara pparb(d) and pparg and effects on gene expression;Pyruvate metabolism and Citric Acid (TCA) cycle;Import of palmitoyl-CoA into the mitochondrial matrix;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription;Endogenous sterols;The citric acid (TCA) cycle and respiratory electron transport;Cytochrome P450 - arranged by substrate type;Biological oxidations;Metabolism;Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol;Transcriptional regulation of white adipocyte differentiation;Synthesis of bile acids and bile salts via 27-hydroxycholesterol;Synthesis of bile acids and bile salts;Recycling of bile acids and salts;Bile acid and bile salt metabolism;Fatty acid metabolism;Metabolism of steroids;degradation of the rar and rxr by the proteasome;Signaling by Retinoic Acid;Signaling by Nuclear Receptors;a6b1 and a6b4 Integrin signaling;RXR and RAR heterodimerization with other nuclear receptor;TNFalpha;Retinoic acid receptors-mediated signaling;Regulation of Androgen receptor activity (Consensus)

Recessive Scores

• pRec: 0.762

Intolerance Scores

• loftool: 0.0143
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.12

Haploinsufficiency Scores

• pHI: 0.725
• hipred: Y
• hipred_score: 0.783
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rxra
• 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); homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; muscle phenotype; digestive/alimentary 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); limbs/digits/tail phenotype; pigmentation 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; 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); normal phenotype; reproductive system phenotype; respiratory system phenotype; liver/biliary system phenotype; embryo phenotype; renal/urinary system phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;in utero embryonic development;maternal placenta development;transcription initiation from RNA polymerase II promoter;vitamin metabolic process;embryo implantation;cholesterol metabolic process;bile acid and bile salt transport;modulation by virus of host morphology or physiology;regulation of lipid metabolic process;response to retinoic acid;peroxisome proliferator activated receptor signaling pathway;camera-type eye development;steroid hormone mediated signaling pathway;positive regulation of transcription by RNA polymerase II;positive regulation of translational initiation by iron;retinoic acid receptor signaling pathway;protein homotetramerization;ventricular cardiac muscle tissue morphogenesis;ventricular cardiac muscle cell differentiation;cardiac muscle cell proliferation;secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development;regulation of branching involved in prostate gland morphogenesis
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;protein-containing complex;receptor complex;RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;retinoic acid binding;DNA binding;double-stranded DNA binding;DNA-binding transcription factor activity;steroid hormone receptor activity;transcription coactivator activity;nuclear receptor activity;protein binding;zinc ion binding;nuclear receptor binding;enzyme binding;chromatin DNA binding;signaling receptor activity;peptide binding;vitamin D receptor binding;sequence-specific DNA binding;transcription regulatory region DNA binding;retinoic acid-responsive element binding;protein heterodimerization activity;DBD domain binding;LBD domain binding;vitamin D response element binding