RAB39A

protein-coding

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

Gene summary

Enables G protein activity. Involved in autophagosome-lysosome fusion; phagosome acidification; and phagosome-lysosome fusion. Located in autolysosome membrane and phagocytic vesicle. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

RAB39

MANE transcript

NM_017516.3

Inheritance

—

ClinVar variants

U:12B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr11:107,928,448-107,963,482

External References & Databases

Ensembl (ENSG00000179331)

Transcript & Mutation Effects

hg38 • Region Span ~35.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RAB39A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017516.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			12 clinvar			12
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	12	1	0	13

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017516.3	RefSeq	NP_059986.1	2	MANE Select
ENST00000320578.3	Ensembl	ENSP00000322594.2	2	MANE Select
ENST00001143304.1	Ensembl	ENSP00000806840.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification
Metabolism of proteins
Rab regulation of trafficking

Biological Process

intracellular protein transport
autophagy
Rab protein signal transduction
phagosome acidification
phagosome-lysosome fusion

Molecular Function

GTPase activity
protein binding
GTP binding

Cellular Component

Golgi membrane
lysosome
cytosol
plasma membrane
phagocytic vesicle membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000320578
Coding exons: 2
Length: 34980
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125748
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.14	84	119	0.706	0.00000598	1396
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

RVIS EVS: -0.03
RVIS percentile EVS: 51.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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