RAB1A

RAB1A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 2:65070696-65130331

Previous symbols: [ "RAB1" ]

Links

ENSG00000138069 ∙ NCBI:5861 ∙ OMIM:179508 ∙ HGNC:9758 ∙ Uniprot:P62820 ∙ 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 RAB1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB1A 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			2		1	3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			48	11	8	67
Total	0	0	50	11	9

Variants in RAB1A

This is a list of pathogenic ClinVar variants found in the RAB1A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-65071461-A-C		not specified	Uncertain significance (Feb 21, 2024)
2-65071481-G-A		not specified	Uncertain significance (Sep 29, 2022)
2-65071614-C-T		not specified	Uncertain significance (Nov 06, 2023)
2-65071686-G-A		not specified	Uncertain significance (Dec 14, 2023)
2-65071692-C-T		not specified	Uncertain significance (Oct 26, 2022)
2-65071698-C-G		not specified	Uncertain significance (Dec 20, 2023)
2-65071737-C-T		not specified	Uncertain significance (Jul 14, 2021)
2-65071746-G-A			Benign (Jun 06, 2018)
2-65071789-C-T			Likely benign (Dec 31, 2019)
2-65071886-A-G		not specified	Uncertain significance (Jun 06, 2023)
2-65071941-T-C		not specified	Uncertain significance (Nov 08, 2022)
2-65071961-C-G		not specified	Uncertain significance (Jul 12, 2022)
2-65071983-A-G		not specified	Uncertain significance (Oct 26, 2022)
2-65072018-C-G		not specified	Uncertain significance (Oct 29, 2021)
2-65072031-G-C		not specified	Uncertain significance (May 16, 2024)
2-65072050-C-A		not specified	Likely benign (Dec 21, 2023)
2-65072052-T-C		not specified	Uncertain significance (Jan 09, 2023)
2-65072054-G-A		not specified	Uncertain significance (Dec 28, 2022)
2-65072058-G-A		not specified	Uncertain significance (Mar 29, 2022)
2-65072060-C-T		not specified	Uncertain significance (Nov 10, 2022)
2-65072070-C-T		not specified	Uncertain significance (Jul 20, 2021)
2-65072165-T-C		not specified	Uncertain significance (Oct 25, 2023)
2-65072196-T-A			Benign (Dec 31, 2019)
2-65072231-C-A		not specified	Uncertain significance (Oct 10, 2023)
2-65072298-C-T		not specified	Uncertain significance (Nov 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB1A	protein_coding	protein_coding	ENST00000409784	6	59406

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.823	0.176	121784	0	3	121787	0.0000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.31	37	103	0.360	0.00000524	1340
Missense in Polyphen		5	37.844	0.13212		547
Synonymous	-0.794	43	36.9	1.17	0.00000203	378
Loss of Function	2.65	1	10.1	0.0992	5.07e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000593	0.0000569
Finnish	0.00	0.00
European (Non-Finnish)	0.0000194	0.0000182
Middle Eastern	0.0000593	0.0000569
South Asian	0.00	0.00
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. RAB1A regulates vesicular protein transport from the endoplasmic reticulum (ER) to the Golgi compartment and on to the cell surface, and plays a role in IL-8 and growth hormone secretion. Regulates the level of CASR present at the cell membrane. Plays a role in cell adhesion and cell migration, via its role in protein trafficking. Plays a role in autophagosome assembly and cellular defense reactions against pathogenic bacteria. Plays a role in microtubule-dependent protein transport by early endosomes and in anterograde melanosome transport. {ECO:0000269|PubMed:20639577, ECO:0000269|PubMed:20861236, ECO:0000269|PubMed:21303926, ECO:0000269|PubMed:22939626}.
• Pathway: Legionellosis - Homo sapiens (human);Bisphosphonate Pathway, Pharmacodynamics;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Golgi Cisternae Pericentriolar Stack Reorganization;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Rab regulation of trafficking;Mitotic Prophase;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;M Phase;RAB GEFs exchange GTP for GDP on RABs;Cell Cycle;RAB geranylgeranylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Cell Cycle, Mitotic;PLK1 signaling events;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.248

Intolerance Scores

• rvis_EVS: 0.3
• rvis_percentile_EVS: 71.81

Haploinsufficiency Scores

• pHI: 0.668
• hipred: Y
• hipred_score: 0.656
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.689

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab1a

Gene ontology

• Biological process: autophagosome assembly;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;endocytosis;autophagy;Golgi organization;vesicle-mediated transport;cell migration;virion assembly;growth hormone secretion;melanosome transport;Rab protein signal transduction;substrate adhesion-dependent cell spreading;defense response to bacterium;post-translational protein modification;vesicle transport along microtubule;COPII vesicle coating;cilium assembly;interleukin-8 secretion;COPII-coated vesicle cargo loading;establishment of endothelial intestinal barrier;positive regulation of glycoprotein metabolic process;positive regulation of ubiquitin protein ligase activity
• Cellular component: Golgi membrane;early endosome;endoplasmic reticulum membrane;Golgi apparatus;cytosol;transport vesicle membrane;melanosome;extracellular exosome
• Molecular function: GTPase activity;protein binding;GTP binding;cadherin binding