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GeneBe

RXRG

retinoid X receptor gamma, the group of Retinoid X receptors

Basic information

Region (hg38): 1:165400921-165445355

Links

ENSG00000143171NCBI:6258OMIM:180247HGNC:10479Uniprot:P48443AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RXRG 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
0
missense
12
clinvar
1
clinvar
13
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
2
clinvar
2
Total 0 0 14 1 0

Variants in RXRG

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

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

Position Type Phenotype Significance ClinVar
1-165401297-A-G Inborn genetic diseases Uncertain significance (Jul 25, 2023)2613444
1-165406827-G-T Inborn genetic diseases Uncertain significance (Aug 29, 2023)2621937
1-165406872-T-C Inborn genetic diseases Uncertain significance (Jul 20, 2022)2392352
1-165408230-G-T Inborn genetic diseases Uncertain significance (Mar 20, 2023)2534134
1-165410774-C-T Inborn genetic diseases Uncertain significance (Feb 22, 2023)2487311
1-165411030-C-T Inborn genetic diseases Uncertain significance (Mar 20, 2023)2526785
1-165411049-G-C Inborn genetic diseases Likely benign (Oct 04, 2022)2403661
1-165411082-C-T Inborn genetic diseases Uncertain significance (Aug 30, 2022)2382035
1-165419918-C-T Inborn genetic diseases Uncertain significance (Apr 05, 2023)2561121
1-165419957-G-T Inborn genetic diseases Uncertain significance (Jul 09, 2021)2235513
1-165419963-C-G Inborn genetic diseases Uncertain significance (Feb 03, 2022)2275929
1-165419966-G-T Inborn genetic diseases Uncertain significance (May 06, 2022)2403879
1-165428805-G-C Inborn genetic diseases Uncertain significance (Jan 26, 2023)2479492
1-165428834-G-T Inborn genetic diseases Uncertain significance (Jul 12, 2023)2596025
1-165428846-C-T Inborn genetic diseases Uncertain significance (Nov 09, 2021)2259762

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RXRGprotein_codingprotein_codingENST00000359842 1044275
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4240.576125735091257440.0000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.591952680.7270.00001473013
Missense in Polyphen78150.180.519361644
Synonymous-0.59410799.51.080.00000541913
Loss of Function3.45522.80.2190.00000137257

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.0002180.000217
Finnish0.000.00
European (Non-Finnish)0.00001770.0000176
Middle Eastern0.0002180.000217
South Asian0.00009800.0000980
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) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid (By similarity). {ECO:0000250}.;
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;Nuclear Receptors;Adipogenesis;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)

Recessive Scores

pRec
0.606

Intolerance Scores

loftool
0.0880
rvis_EVS
-0.85
rvis_percentile_EVS
11.06

Haploinsufficiency Scores

pHI
0.645
hipred
Y
hipred_score
0.765
ghis
0.591

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.996

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rxrg
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); normal 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); muscle 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
nucleoplasm
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;steroid hormone receptor activity;nuclear receptor activity;protein binding;zinc ion binding;sequence-specific DNA binding