RRAGA
Ras related GTP binding A, the group of Ras related GTP binding proteins
Basic information
Region (hg38): 9:19049427-19051025
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 RRAGA 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 | 3 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 2 | |||||
| Total | 0 | 0 | 6 | 2 | 3 |
Variants in RRAGA
This is a list of pathogenic ClinVar variants found in the RRAGA region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-19049514-T-G | Benign (Apr 10, 2019) | |||
| 9-19049598-C-A | Benign (Sep 05, 2018) | |||
| 9-19049667-A-G | not specified | Uncertain significance (Apr 08, 2022) | ||
| 9-19050011-C-T | not specified | Uncertain significance (Aug 17, 2022) | ||
| 9-19050020-A-G | not specified | Uncertain significance (Nov 28, 2023) | ||
| 9-19050073-C-G | not specified | Uncertain significance (Nov 19, 2022) | ||
| 9-19050103-G-C | Benign (May 20, 2023) | |||
| 9-19050325-G-A | Benign/Likely benign (Aug 27, 2023) | |||
| 9-19050555-A-G | Uncertain significance (Sep 05, 2023) | |||
| 9-19050568-G-C | Likely benign (Apr 12, 2018) | |||
| 9-19050581-C-T | not specified | Uncertain significance (Jul 17, 2023) |
GnomAD
Source:
| 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:
- 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