RARG

retinoic acid receptor gamma, the group of Retinoic acid receptors

Basic information

Region (hg38): 12:53210566-53232980

Links

ENSG00000172819 ∙ NCBI:5916 ∙ OMIM:180190 ∙ HGNC:9866 ∙ Uniprot:P13631 ∙ 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 RARG gene.

• Inborn genetic diseases (2 variants)
• not provided (1 variants)
• Irido-corneo-trabecular dysgenesis (1 variants)

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			2	1	1	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	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)
12-53215385-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: gnomAD

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: 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. 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