RAB13

RAB13, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 1:153981617-153986358

Links

ENSG00000143545

∙ NCBI:5872 ∙ OMIM:602672 ∙ HGNC:9762 ∙ Uniprot:P51153 ∙ 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 RAB13 gene.

not_specified (16 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002870.5. 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				1 clinvar		1
missense			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB13	protein_coding	protein_coding	ENST00000368575	8	4708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0247	0.963	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	86	119	0.723	0.00000677	1342
Missense in Polyphen		38	63.778	0.59582		704
Synonymous	0.575	41	46.0	0.892	0.00000269	370
Loss of Function	2.20	5	13.8	0.362	7.40e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. That Rab is involved in endocytic recycling and regulates the transport to the plasma membrane of transmembrane proteins like the tight junction protein OCLN/occludin. Thereby, it regulates the assembly and the activity of tight junctions. Moreover, it may also regulate tight junction assembly by activating the PKA signaling pathway and by reorganizing the actin cytoskeleton through the activation of the downstream effectors PRKACA and MICALL2 respectively. Through its role in tight junction assembly, may play a role in the establishment of Sertoli cell barrier. Plays also a role in angiogenesis through regulation of endothelial cells chemotaxis. Also involved in neurite outgrowth. Has also been proposed to play a role in post-Golgi membrane trafficking from the TGN to the recycling endosome. Finally, it has been involved in insulin- induced transport to the plasma membrane of the glucose transporter GLUT4 and therefore may play a role in glucose homeostasis. {ECO:0000269|PubMed:12058051, ECO:0000269|PubMed:15096524, ECO:0000269|PubMed:15528189, ECO:0000269|PubMed:16525024, ECO:0000269|PubMed:18779367, ECO:0000269|PubMed:20008558}.;
Pathway: Tight junction - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation;Translocation of GLUT4 to the plasma membrane (Consensus)

Recessive Scores

pRec: 0.149

Intolerance Scores

loftool: 0.353
rvis_EVS: 0.22
rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

pHI: 0.0752
hipred: Y
hipred_score: 0.818
ghis: 0.539

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rab13
Phenotype

Zebrafish Information Network

Gene name: rab13
Affected structure: dorsal longitudinal anastomotic vessel
Phenotype tag: abnormal
Phenotype quality: aplastic

Gene ontology

Biological process: intracellular protein transport;protein kinase A signaling;endosomal transport;cortical actin cytoskeleton organization;neuron projection development;endocytic recycling;Rab protein signal transduction;cellular response to insulin stimulus;endothelial cell chemotaxis;post-translational protein modification;trans-Golgi network to recycling endosome transport;bicellular tight junction assembly;protein localization to plasma membrane;establishment of Sertoli cell barrier
Cellular component: Golgi apparatus;trans-Golgi network;cytosol;plasma membrane;bicellular tight junction;lateral plasma membrane;lamellipodium;cell junction;endocytic vesicle;cytoplasmic vesicle membrane;cytoplasmic vesicle;insulin-responsive compartment;neuron projection;recycling endosome;recycling endosome membrane;extracellular exosome
Molecular function: GTPase activity;protein binding;GTP binding