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GeneBe

RIT2

Ras like without CAAX 2, the group of RAS type GTPase family

Basic information

Region (hg38): 18:42743226-43115691

Previous symbols: [ "RIN" ]

Links

ENSG00000152214NCBI:6014OMIM:609592HGNC:10017Uniprot:Q99578AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RIT2 gene.

  • Inborn genetic diseases (6 variants)
  • not provided (1 variants)

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
6
clinvar
6
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 6 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 Inborn genetic diseases Uncertain significance (Feb 16, 2023)2468710
18-42923585-T-C Inborn genetic diseases Uncertain significance (Mar 24, 2023)2529401
18-42923653-C-G Inborn genetic diseases Uncertain significance (Nov 18, 2022)2328221
18-42923770-GA-G Benign (Aug 04, 2017)769441
18-43115446-A-G Inborn genetic diseases Uncertain significance (Sep 01, 2021)2247838
18-43115491-G-T Inborn genetic diseases Uncertain significance (Nov 23, 2022)2393597
18-43115500-G-C Inborn genetic diseases Uncertain significance (May 24, 2023)2517126

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RIT2protein_codingprotein_codingENST00000326695 5372466
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0006320.7471257170271257440.000107
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.890951230.7740.000006441441
Missense in Polyphen3258.7930.54428663
Synonymous0.6333742.20.8760.00000208388
Loss of Function0.95069.090.6603.81e-7125

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001530.000149
Ashkenazi Jewish0.000.00
East Asian0.0001640.000163
Finnish0.0003230.000323
European (Non-Finnish)0.00007070.0000703
Middle Eastern0.0001640.000163
South Asian0.00003270.0000327
Other0.0006580.000652

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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