RXRG
retinoid X receptor gamma, the group of Retinoid X receptors
Basic information
Region (hg38): 1:165400921-165445355
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 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 | not specified | Uncertain significance (Jul 25, 2023) | ||
| 1-165406827-G-T | not specified | Uncertain significance (Aug 29, 2023) | ||
| 1-165406872-T-C | not specified | Uncertain significance (Jul 20, 2022) | ||
| 1-165408230-G-T | not specified | Uncertain significance (Mar 20, 2023) | ||
| 1-165410774-C-T | not specified | Uncertain significance (Feb 22, 2023) | ||
| 1-165411030-C-T | not specified | Uncertain significance (Mar 20, 2023) | ||
| 1-165411049-G-C | not specified | Likely benign (Oct 04, 2022) | ||
| 1-165411082-C-T | not specified | Uncertain significance (Aug 30, 2022) | ||
| 1-165419909-C-A | not specified | Uncertain significance (Dec 27, 2023) | ||
| 1-165419918-C-T | not specified | Uncertain significance (Apr 05, 2023) | ||
| 1-165419957-G-T | not specified | Uncertain significance (Jul 09, 2021) | ||
| 1-165419963-C-G | not specified | Uncertain significance (Feb 03, 2022) | ||
| 1-165419966-G-T | not specified | Uncertain significance (May 06, 2022) | ||
| 1-165428805-G-C | not specified | Uncertain significance (Jan 26, 2023) | ||
| 1-165428834-G-T | not specified | Uncertain significance (Jul 12, 2023) | ||
| 1-165428846-C-T | not specified | Uncertain significance (Nov 09, 2021) | ||
| 1-165428917-C-A | not specified | Uncertain significance (Jun 21, 2021) | ||
| 1-165428925-C-T | not specified | Uncertain significance (Nov 03, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RXRG | protein_coding | protein_coding | ENST00000359842 | 10 | 44275 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.424 | 0.576 | 125735 | 0 | 9 | 125744 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.59 | 195 | 268 | 0.727 | 0.0000147 | 3013 |
| Missense in Polyphen | 78 | 150.18 | 0.51936 | 1644 | ||
| Synonymous | -0.594 | 107 | 99.5 | 1.08 | 0.00000541 | 913 |
| Loss of Function | 3.45 | 5 | 22.8 | 0.219 | 0.00000137 | 257 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000218 | 0.000217 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.000218 | 0.000217 |
| South Asian | 0.0000980 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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