RAB6A

RAB6A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 11:73675638-73761137

Previous symbols: [ "RAB6" ]

Links

ENSG00000175582 ∙ NCBI:5870 ∙ OMIM:179513 ∙ HGNC:9786 ∙ Uniprot:P20340 ∙ 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 RAB6A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB6A 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				1	1	2
missense			2		1	3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	1	2

Variants in RAB6A

This is a list of pathogenic ClinVar variants found in the RAB6A region.

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

Position	Type	Phenotype	Significance	ClinVar
11-73677911-C-G			Benign (Dec 31, 2019)
11-73679671-T-G		not specified	Uncertain significance (Apr 06, 2023)
11-73716319-G-A			Likely benign (Jan 01, 2023)
11-73718840-G-T			Benign (Dec 31, 2019)
11-73760615-G-T		not specified	Uncertain significance (Jul 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB6A	protein_coding	protein_coding	ENST00000310653	8	85500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.952	0.0476	125741	0	2	125743	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.50	41	117	0.350	0.00000613	1376
Missense in Polyphen		7	29.634	0.23622		381
Synonymous	0.891	31	38.0	0.816	0.00000191	373
Loss of Function	3.22	1	14.0	0.0716	7.23e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein transport. Regulator of membrane traffic from the Golgi apparatus towards the endoplasmic reticulum (ER). Has a low GTPase activity. Involved in COPI-independent retrograde transport from the Golgi to the ER (PubMed:25962623). {ECO:0000269|PubMed:25962623}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Neutrophil degranulation;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Rab regulation of trafficking;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Intolerance Scores

• loftool: 0.286
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.935

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab6a
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: intracellular protein transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;intra-Golgi vesicle-mediated transport;viral process;peptidyl-cysteine methylation;antigen processing and presentation;Rab protein signal transduction;protein localization to Golgi apparatus;early endosome to Golgi transport;retrograde transport, endosome to Golgi;neutrophil degranulation;minus-end-directed organelle transport along microtubule
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;Golgi apparatus;trans-Golgi network;cytosol;plasma membrane;membrane;secretory granule membrane;cytoplasmic vesicle;trans-Golgi network membrane;extracellular exosome;endosome to plasma membrane transport vesicle
• Molecular function: GTPase activity;protein binding;GTP binding;protein domain specific binding;myosin V binding