RXRB

retinoid X receptor beta, the group of Retinoid X receptors

Basic information

Region (hg38): 6:33193588-33200665

Links

ENSG00000204231 ∙ NCBI:6257 ∙ OMIM:180246 ∙ HGNC:10478 ∙ Uniprot:P28702 ∙ 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 RXRB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RXRB 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				3	2	5
missense			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	17	5	2

Variants in RXRB

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

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

Position	Type	Phenotype	Significance	ClinVar
6-33194699-G-A		not specified	Uncertain significance (May 06, 2024)
6-33194833-G-GGGTGGA		RXRB-related disorder	Benign (Dec 31, 2019)
6-33194980-G-C		RXRB-related disorder	Likely benign (May 08, 2019)
6-33195026-C-T		not specified	Uncertain significance (Oct 04, 2022)
6-33195418-C-T		not specified	Uncertain significance (Jan 23, 2024)
6-33195620-G-A		RXRB-related disorder	Likely benign (Jul 10, 2019)
6-33195632-G-A		RXRB-related disorder	Likely benign (Jul 10, 2019)
6-33195674-G-A		RXRB-related disorder	Benign (Sep 27, 2019)
6-33196454-T-C		not specified	Uncertain significance (Apr 18, 2024)
6-33196456-C-T		not specified	Uncertain significance (May 23, 2023)
6-33196472-C-T		not specified	Likely benign (Mar 21, 2023)
6-33196553-C-G		not specified	Uncertain significance (Jun 13, 2022)
6-33197947-G-C		RXRB-related disorder	Benign (Jun 18, 2019)
6-33198324-G-A		RXRB-related disorder	Benign (Jun 27, 2019)
6-33198386-C-T		not specified	Uncertain significance (Dec 06, 2021)
6-33199179-C-T		not specified	Uncertain significance (Oct 04, 2022)
6-33199227-G-A		not specified	Uncertain significance (Sep 12, 2023)
6-33199270-G-C		not specified	Uncertain significance (Jun 01, 2023)
6-33199270-G-T		not specified	Uncertain significance (Feb 07, 2023)
6-33199285-G-T		not specified	Uncertain significance (Jan 16, 2024)
6-33199342-G-A		RXRB-related disorder	Likely benign (Feb 01, 2023)
6-33199345-G-A		not specified	Uncertain significance (Mar 31, 2023)
6-33199390-G-A		not specified	Uncertain significance (Jan 16, 2024)
6-33200281-C-G		not specified	Uncertain significance (Dec 20, 2023)
6-33200287-C-G		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RXRB	protein_coding	protein_coding	ENST00000374685	10	7266

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00281	123951	0	5	123956	0.0000202

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.42	129	294	0.439	0.0000167	3394
Missense in Polyphen		42	145.88	0.28791		1531
Synonymous	2.51	78	112	0.698	0.00000568	1157
Loss of Function	4.11	1	21.7	0.0462	0.00000112	250

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000180	0.0000180
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). {ECO:0000269|PubMed:1310259}.
• Pathway: Non-small cell lung cancer - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Adipocytokine signaling pathway - Homo sapiens (human);Small cell lung cancer - 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);Thyroid cancer - Homo sapiens (human);NHR;Vitamin D Metabolism;Nuclear Receptors;PPAR signaling pathway;Vitamin A and Carotenoid Metabolism;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription;Signaling by Retinoic Acid;Signaling by Nuclear Receptors;a6b1 and a6b4 Integrin signaling;RXR and RAR heterodimerization with other nuclear receptor;Retinoic acid receptors-mediated signaling;Regulation of Androgen receptor activity (Consensus)

Intolerance Scores

• loftool: 0.140
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.322
• hipred: Y
• hipred_score: 0.785
• ghis: 0.684

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: Rxrb
• Phenotype: hematopoietic 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); reproductive 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); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; immune system phenotype; vision/eye 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); hearing/vestibular/ear 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

Gene ontology

• Biological process: transcription initiation from RNA polymerase II promoter;steroid hormone mediated signaling pathway;positive regulation of transcription by RNA polymerase II;retinoic acid receptor signaling pathway
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;steroid hormone receptor activity;transcription coactivator activity;nuclear receptor activity;protein binding;zinc ion binding