RRAGA

Ras related GTP binding A, the group of Ras related GTP binding proteins

Basic information

Region (hg38): 9:19049427-19051025

Links

ENSG00000155876 ∙ NCBI:10670 ∙ OMIM:612194 ∙ HGNC:16963 ∙ Uniprot:Q7L523 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cataract (Strong), mode of inheritance: AD

ClinVar

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

• not_specified (14 variants)
• not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RRAGA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006570.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	2	1	4
missense			15			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	2	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RRAGA	protein_coding	protein_coding	ENST00000380527	1	1648

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.356	0.633	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.99	63	174	0.363	0.00000820	2096
Missense in Polyphen		5	55.565	0.089984		700
Synonymous	-1.75	88	69.5	1.27	0.00000337	605
Loss of Function	2.13	2	8.83	0.227	4.00e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide-binding protein that plays a crucial role in the cellular response to amino acid availability through regulation of the mTORC1 signaling cascade. Forms heterodimeric Rag complexes with RRAGC or RRAGD and cycles between an inactive GDP-bound and an active GTP-bound form. In its active form participates in the relocalization of mTORC1 to the lysosomes and its subsequent activation by the GTPase RHEB. Involved in the RCC1/Ran-GTPase pathway. May play a direct role in a TNF-alpha signaling pathway leading to induction of cell death. May alternatively act as a cellular target for adenovirus E3-14.7K, an inhibitor of TNF-alpha functions, thereby affecting cell death. {ECO:0000269|PubMed:20381137, ECO:0000269|PubMed:25936802, ECO:0000269|PubMed:8995684, ECO:0000269|PubMed:9394008}.
• Pathway: mTOR signaling pathway - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Target Of Rapamycin (TOR) Signaling;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;Post-translational protein modification;Metabolism of proteins;RNA Polymerase II Transcription;mTORC1-mediated signalling;Energy dependent regulation of mTOR by LKB1-AMPK;mTOR signalling;TP53 Regulates Metabolic Genes;Macroautophagy;Cellular responses to external stimuli;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Transcriptional Regulation by TP53;Protein ubiquitination;Intracellular signaling by second messengers;mTOR signaling pathway;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.299
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.0546
• hipred: N
• hipred_score: 0.447
• ghis: 0.613

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rraga
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; immune system 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); 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); neoplasm; embryo phenotype

Gene ontology

• Biological process: apoptotic process;cell cycle arrest;cell death;cellular response to starvation;regulation of autophagy;negative regulation of autophagy;regulation of macroautophagy;protein ubiquitination;modulation by virus of host morphology or physiology;positive regulation of TOR signaling;cellular response to amino acid starvation;cellular protein localization;positive regulation of cytolysis;cellular response to amino acid stimulus;positive regulation of TORC1 signaling
• Cellular component: nucleus;cytoplasm;lysosome;lysosomal membrane;cytosol;EGO complex;GATOR1 complex;Gtr1-Gtr2 GTPase complex
• Molecular function: GTPase activity;protein binding;GTP binding;ubiquitin protein ligase binding;protein homodimerization activity;protein heterodimerization activity;phosphoprotein binding