RRAGD
Basic information
Region (hg38): 6:89364616-89412273
Links
Phenotypes
GenCC
Source:
- hypomagnesemia 7, renal, with or without dilated cardiomyopathy (Moderate), mode of inheritance: AD
- hypomagnesemia 7, renal, with or without dilated cardiomyopathy (Strong), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (27 variants)
- not_provided (5 variants)
- Hypomagnesemia_7,_renal,_with_or_without_dilated_cardiomyopathy (5 variants)
- HYPOMAGNESEMIA_7,_RENAL,_WITH_DILATED_CARDIOMYOPATHY (2 variants)
- HYPOMAGNESEMIA_7,_RENAL,_WITHOUT_DILATED_CARDIOMYOPATHY (2 variants)
- RRAGD-related_disorder (1 variants)
- not_specified (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RRAGD gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021244.5. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 30 | 39 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 7 | 1 | 31 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RRAGD | protein_coding | protein_coding | ENST00000369415 | 7 | 47635 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.820 | 0.180 | 125725 | 0 | 1 | 125726 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.20 | 119 | 208 | 0.571 | 0.0000103 | 2671 |
| Missense in Polyphen | 18 | 61.372 | 0.2933 | 758 | ||
| Synonymous | 1.13 | 65 | 77.7 | 0.837 | 0.00000427 | 730 |
| Loss of Function | 3.03 | 2 | 14.4 | 0.139 | 6.51e-7 | 202 |
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) | 0.00000879 | 0.00000879 |
| 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 forming heterodimeric Rag complexes required for the amino acid-induced relocalization of mTORC1 to the lysosomes and its subsequent activation by the GTPase RHEB. This is a crucial step in the activation of the TOR signaling cascade by amino acids. {ECO:0000269|PubMed:20381137}.;
- 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;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;Intracellular signaling by second messengers;mTOR signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.0712
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- 0.211
- hipred
- Y
- hipred_score
- 0.715
- ghis
- 0.517
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.838
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rragd
- Phenotype
Gene ontology
- Biological process
- cell cycle arrest;cellular response to starvation;regulation of autophagy;regulation of macroautophagy;positive regulation of TOR signaling;cellular protein localization;cellular response to amino acid stimulus;cellular response to leucine;positive regulation of TORC1 signaling;cellular response to leucine starvation
- Cellular component
- nucleus;nucleoplasm;cytoplasm;lysosome;centrosome;cytosol;EGO complex;Gtr1-Gtr2 GTPase complex
- Molecular function
- GTPase activity;protein binding;GTP binding;GDP binding;protein heterodimerization activity;GTPase binding