RAB43

RAB43, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 3:129087568-129122801

Links

ENSG00000172780 ∙ NCBI:339122 ∙ ∙ HGNC:19983 ∙ Uniprot:Q86YS6 ∙ 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 RAB43 gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB43 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			2
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	0	0

Variants in RAB43

This is a list of pathogenic ClinVar variants found in the RAB43 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-129091125-T-C		not specified	Likely benign (Dec 15, 2023)
3-129091194-T-C		not specified	Likely benign (Jan 16, 2024)
3-129091202-G-A		not specified	Uncertain significance (Oct 05, 2022)
3-129091289-A-G		not specified	Uncertain significance (May 30, 2023)
3-129092570-G-C		RAB43-related disorder	Uncertain significance (Jan 22, 2024)
3-129092596-A-C		RAB43-related disorder	Likely benign (Mar 08, 2022)
3-129094987-G-A		RAB43-related disorder	Likely benign (Feb 23, 2022)
3-129095014-C-T		RAB43-related disorder	Likely benign (Feb 01, 2023)
3-129095017-A-G		RAB43-related disorder	Likely benign (Dec 27, 2022)
3-129121293-C-A		not specified	Uncertain significance (Jan 04, 2024)
3-129121439-G-A		RAB43-related disorder	Likely benign (Mar 22, 2022)
3-129121478-C-T		RAB43-related disorder	Benign (Jun 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB43	protein_coding	protein_coding	ENST00000315150	3	35233

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.562	0.427	125733	0	3	125736	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	83	126	0.657	0.00000723	1379
Missense in Polyphen		26	46.954	0.55373		531
Synonymous	0.269	55	57.6	0.955	0.00000370	417
Loss of Function	2.04	1	6.70	0.149	2.86e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000668	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 set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. The low intrinsic GTPase activity of RAB43 is activated by USP6NL. Involved in retrograde transport from the endocytic pathway to the Golgi apparatus. Involved in the transport of Shiga toxin from early and recycling endosomes to the trans-Golgi network. Required for the structural integrity of the Golgi complex. Plays a role in the maturation of phagosomes that engulf pathogens, such as S.aureus and M.tuberculosis. {ECO:0000269|PubMed:17562788, ECO:0000269|PubMed:17684057, ECO:0000269|PubMed:18664496, ECO:0000269|PubMed:21255211}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.0846

Intolerance Scores

• loftool: 0.462
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.0556
• hipred: Y
• hipred_score: 0.549
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0807

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab43
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;virion assembly;Rab protein signal transduction;retrograde transport, plasma membrane to Golgi;cellular response to interferon-gamma;phagosome maturation;toxin transport
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;Golgi apparatus;phagocytic vesicle membrane;trans-Golgi network membrane;phagocytic vesicle;extracellular exosome
• Molecular function: GTPase activity;protein binding;GTP binding