RARG
retinoic acid receptor gamma, the group of Retinoic acid receptors
Basic information
Region (hg38): 12:53210567-53232980
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RARG 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 1 | 1 |
Variants in RARG
This is a list of pathogenic ClinVar variants found in the RARG region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-53211761-G-A | Benign (Jul 11, 2019) | |||
| 12-53214571-C-G | not specified | Uncertain significance (Jan 03, 2024) | ||
| 12-53214571-C-T | not specified | Uncertain significance (May 04, 2023) | ||
| 12-53214587-G-C | not specified | Uncertain significance (Jul 26, 2022) | ||
| 12-53214592-G-A | not specified | Uncertain significance (Apr 24, 2024) | ||
| 12-53215385-C-T | not specified | Uncertain significance (Mar 14, 2023) | ||
| 12-53215734-G-A | Irido-corneo-trabecular dysgenesis | Likely benign (Jan 01, 2013) | ||
| 12-53227464-C-T | not specified | Uncertain significance (Jul 12, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RARG | protein_coding | protein_coding | ENST00000425354 | 8 | 22411 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.995 | 0.00522 | 125719 | 0 | 8 | 125727 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.13 | 127 | 273 | 0.466 | 0.0000160 | 2969 |
| Missense in Polyphen | 31 | 121.86 | 0.2544 | 1238 | ||
| Synonymous | 0.297 | 104 | 108 | 0.964 | 0.00000610 | 909 |
| Loss of Function | 3.94 | 1 | 20.0 | 0.0500 | 0.00000116 | 217 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000170 | 0.000170 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000285 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| 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. In the absence of ligand, acts mainly as an activator of gene expression due to weak binding to corepressors. Required for limb bud development. In concert with RARA or RARB, required for skeletal growth, matrix homeostasis and growth plate function (By similarity). {ECO:0000250}.;
- Pathway
- NHR;Nuclear Receptors;Mesodermal Commitment Pathway;Nuclear Receptors in Lipid Metabolism and Toxicity;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;RXR and RAR heterodimerization with other nuclear receptor;Retinoic acid receptors-mediated signaling
(Consensus)
Recessive Scores
- pRec
- 0.221
Intolerance Scores
- loftool
- 0.0555
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.32
Haploinsufficiency Scores
- pHI
- 0.547
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.648
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rarg
- 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); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; vision/eye 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); 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; embryo phenotype; respiratory system phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; digestive/alimentary 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;
Zebrafish Information Network
- Gene name
- rarga
- Affected structure
- pharyngeal arch 5
- Phenotype tag
- abnormal
- Phenotype quality
- immature
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;neural tube closure;glandular epithelial cell development;growth plate cartilage chondrocyte growth;transcription initiation from RNA polymerase II promoter;multicellular organism development;positive regulation of cell population proliferation;negative regulation of cell population proliferation;regulation of cell size;hormone-mediated signaling pathway;anterior/posterior pattern specification;cell differentiation;embryonic camera-type eye development;regulation of myelination;negative regulation of chondrocyte differentiation;response to retinoic acid;response to lipid;embryonic hindlimb morphogenesis;multicellular organism growth;positive regulation of apoptotic process;positive regulation of programmed cell death;steroid hormone mediated signaling pathway;regulation of myeloid cell differentiation;positive regulation of transcription by RNA polymerase II;embryonic eye morphogenesis;retinoic acid receptor signaling pathway;gland development;canonical Wnt signaling pathway;face development;bone morphogenesis;epithelium development;trachea cartilage development;prostate gland epithelium morphogenesis;Harderian gland development;cellular response to retinoic acid;cellular response to leukemia inhibitory factor
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;transcription factor complex;integral component of membrane;RNA polymerase II transcription factor complex
- Molecular function
- transcription regulatory region sequence-specific DNA binding;RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;steroid hormone receptor activity;protein binding;transcription factor binding;zinc ion binding;nuclear receptor transcription coactivator activity;signaling receptor activity;retinoid X receptor binding