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GeneBe

RXRB

retinoid X receptor beta, the group of Retinoid X receptors

Basic information

Region (hg38): 6:33193587-33200665

Links

ENSG00000204231NCBI:6257OMIM:180246HGNC:10478Uniprot:P28702AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (12 variants)
  • not provided (2 variants)

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
1
clinvar
1
missense
11
clinvar
1
clinvar
12
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 11 1 1

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
6-33194833-G-GGGTGGA RXRB-related condition Benign (Dec 31, 2019)779906
6-33194980-G-C RXRB-related condition Likely benign (May 08, 2019)3041645
6-33195026-C-T not specified Uncertain significance (Oct 04, 2022)2356807
6-33195418-C-T not specified Uncertain significance (Jan 23, 2024)3157304
6-33195620-G-A RXRB-related condition Likely benign (Jul 10, 2019)3049286
6-33195632-G-A RXRB-related condition Likely benign (Jul 10, 2019)3050300
6-33195674-G-A RXRB-related condition Benign (Oct 16, 2019)1254260
6-33196456-C-T not specified Uncertain significance (May 23, 2023)2514900
6-33196472-C-T not specified Likely benign (Mar 21, 2023)2522153
6-33196553-C-G not specified Uncertain significance (Jun 13, 2022)2295526
6-33197947-G-C RXRB-related condition Benign (Jun 18, 2019)3034436
6-33198324-G-A RXRB-related condition Benign (Jun 27, 2019)3042895
6-33198386-C-T not specified Uncertain significance (Dec 06, 2021)2265161
6-33199179-C-T not specified Uncertain significance (Oct 04, 2022)2373624
6-33199227-G-A not specified Uncertain significance (Sep 12, 2023)2598639
6-33199270-G-C not specified Uncertain significance (Jun 01, 2023)2554623
6-33199270-G-T not specified Uncertain significance (Feb 07, 2023)2482120
6-33199285-G-T not specified Uncertain significance (Jan 16, 2024)3157308
6-33199342-G-A RXRB-related condition Likely benign (Feb 01, 2023)3061577
6-33199345-G-A not specified Uncertain significance (Mar 31, 2023)2531770
6-33199390-G-A not specified Uncertain significance (Jan 16, 2024)3157307
6-33200281-C-G not specified Uncertain significance (Dec 20, 2023)3157306
6-33200287-C-G not specified Uncertain significance (May 24, 2023)2545533
6-33200322-G-C not specified Uncertain significance (Nov 22, 2023)3157305
6-33200424-T-C not specified Uncertain significance (Jan 24, 2024)3157309

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RXRBprotein_codingprotein_codingENST00000374685 107266
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9970.00281123951051239560.0000202
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.421292940.4390.00001673394
Missense in Polyphen42145.880.287911531
Synonymous2.51781120.6980.000005681157
Loss of Function4.11121.70.04620.00000112250

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001240.000123
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001800.0000180
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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