RIT2

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

Basic information

Region (hg38): 18:42743226-43115691

Previous symbols: [ "RIN" ]

Links

ENSG00000152214 ∙ NCBI:6014 ∙ OMIM:609592 ∙ HGNC:10017 ∙ Uniprot:Q99578 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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			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		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)
18-42923653-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: gnomAD

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: 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

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

Mouse Genome Informatics

• Gene name: Rit2

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