RAB39A

RAB39A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 11:107928448-107963482

Previous symbols: [ "RAB39" ]

Links

ENSG00000179331 ∙ NCBI:54734 ∙ OMIM:619558 ∙ HGNC:16521 ∙ Uniprot:Q14964 ∙ 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 RAB39A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB39A 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			3			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	3	0	0

Variants in RAB39A

This is a list of pathogenic ClinVar variants found in the RAB39A region.

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

Position	Type	Phenotype	Significance	ClinVar
11-107928663-G-A		not specified	Uncertain significance (Mar 15, 2024)
11-107928789-G-T		not specified	Uncertain significance (May 11, 2022)
11-107961957-G-T		not specified	Uncertain significance (Jun 29, 2023)
11-107962286-T-C		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB39A	protein_coding	protein_coding	ENST00000320578	2	34980

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000892	0.811	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	84	119	0.706	0.00000598	1396
Missense in Polyphen		24	44.004	0.5454		491
Synonymous	0.119	43	44.0	0.977	0.00000204	432
Loss of Function	1.12	6	9.79	0.613	6.86e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000880	0.0000880
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the maturation and acidification of phagosomes that engulf pathogens, such as S.aureus and M.tuberculosis. Plays a role in vesicular trafficking. Plays a role in the fusion of phagosomes with lysosomes. Negatively regulates LPS-induced autophagosome formation in macrophages possibly by implicating PI3K (PubMed:24349490). May be involved in multiple neurite formation (By similarity). {ECO:0000250|UniProtKB:Q8BHD0, ECO:0000269|PubMed:21255211, ECO:0000269|PubMed:24349490}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Rab regulation of trafficking;Intra-Golgi traffic;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.673
• hipred: N
• hipred_score: 0.379
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab39
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: intracellular protein transport;autophagy;Rab protein signal transduction;phagosome acidification;phagosome-lysosome fusion
• Cellular component: Golgi membrane;lysosome;cytosol;plasma membrane;phagocytic vesicle membrane;phagocytic vesicle
• Molecular function: GTPase activity;protein binding;GTP binding