RIT2
Basic information
Region (hg38): 18:42743227-43115691
Previous symbols: [ "RIN" ]
Links
Phenotypes
GenCC
Source:
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 RIT2 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 0 |
Variants in RIT2
This is a list of pathogenic ClinVar variants found in the RIT2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-42743569-T-G | not specified | Uncertain significance (Feb 16, 2023) | ||
| 18-42743638-A-G | not specified | Uncertain significance (Nov 03, 2023) | ||
| 18-42923585-T-C | not specified | Uncertain significance (Mar 24, 2023) | ||
| 18-42923627-T-C | not specified | Uncertain significance (May 21, 2024) | ||
| 18-42923653-C-G | not specified | Uncertain significance (Nov 18, 2022) | ||
| 18-42923770-GA-G | Benign (Aug 04, 2017) | |||
| 18-42974120-A-G | not specified | Uncertain significance (Dec 14, 2023) | ||
| 18-43115446-A-G | not specified | Uncertain significance (Sep 01, 2021) | ||
| 18-43115471-C-T | not specified | Uncertain significance (Feb 01, 2023) | ||
| 18-43115491-G-T | not specified | Uncertain significance (Nov 23, 2022) | ||
| 18-43115500-G-C | not specified | Uncertain significance (May 24, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RIT2 | protein_coding | protein_coding | ENST00000326695 | 5 | 372466 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000632 | 0.747 | 125717 | 0 | 27 | 125744 | 0.000107 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.890 | 95 | 123 | 0.774 | 0.00000644 | 1441 |
| Missense in Polyphen | 32 | 58.793 | 0.54428 | 663 | ||
| Synonymous | 0.633 | 37 | 42.2 | 0.876 | 0.00000208 | 388 |
| Loss of Function | 0.950 | 6 | 9.09 | 0.660 | 3.81e-7 | 125 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000153 | 0.000149 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000164 | 0.000163 |
| Finnish | 0.000323 | 0.000323 |
| European (Non-Finnish) | 0.0000707 | 0.0000703 |
| Middle Eastern | 0.000164 | 0.000163 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000658 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Binds and exchanges GTP and GDP. Binds and modulates the activation of POU4F1 as gene expression regulator. {ECO:0000250|UniProtKB:P70425}.;
- Pathway
- Signal Transduction;Signalling to p38 via RIT and RIN;Signalling to ERKs;Signaling by NTRK1 (TRKA);Signaling by NTRKs;Signaling by Receptor Tyrosine Kinases;Neurotrophic factor-mediated Trk receptor signaling;Trk receptor signaling mediated by the MAPK pathway
(Consensus)
Recessive Scores
- pRec
- 0.287
Intolerance Scores
- loftool
- 0.685
- rvis_EVS
- 0.19
- rvis_percentile_EVS
- 66.57
Haploinsufficiency Scores
- pHI
- 0.934
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.561
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0282
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rit2
- Phenotype
Gene ontology
- Biological process
- MAPK cascade;adenylate cyclase-activating G protein-coupled receptor signaling pathway;small GTPase mediated signal transduction;Ras protein signal transduction;chemical synaptic transmission;positive regulation of neuron projection development;negative regulation of neuron projection development;regulation of endocytosis;regulation of Cdc42 protein signal transduction;maintenance of protein location in cell;intracellular signal transduction;positive regulation of MAPK cascade;positive regulation of transcription by RNA polymerase II;regulation of calcium-mediated signaling
- Cellular component
- nucleus;cytoplasm;plasma membrane;neuron projection;cell body;membrane raft;dendritic tree
- Molecular function
- chromatin binding;GTPase activity;protein binding;calmodulin binding;GTP binding;semaphorin receptor binding;identical protein binding