RAB39A

Summary

RAB39A (RAB39A, member RAS oncogene family, HGNC:16521) is a protein-coding gene on chromosome 11q22.3, encoding Ras-related protein Rab-39A (Q14964). The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes.

Predicted to enable GTP binding activity and GTPase activity. Involved in phagosome acidification and phagosome-lysosome fusion. Located in phagocytic vesicle.

Source: NCBI Gene 54734 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 15 total
• Druggable target: yes
• MANE Select transcript: NM_017516

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16521
Approved symbol	RAB39A
Name	RAB39A, member RAS oncogene family
Location	11q22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000179331
Ensembl biotype	protein_coding
OMIM	619558
Entrez	54734

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000320578

RefSeq mRNA: 1 — MANE Select: NM_017516 NM_017516

CCDS: CCDS8338

Canonical transcript exons

ENST00000320578 — 2 exons

Exon	Start	End
ENSE00001241448	107961946	107963482
ENSE00001241454	107928448	107928795

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 82.73.

FANTOM5 (CAGE): breadth broad, TPM avg 3.5862 / max 125.4906, expressed in 676 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
116511	2.9685	650
116512	0.3600	197
116513	0.2577	130

Top tissues by expression

237 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.73	gold quality
monocyte	CL:0000576	78.17	gold quality
leukocyte	CL:0000738	77.26	gold quality
cortical plate	UBERON:0005343	76.90	gold quality
islet of Langerhans	UBERON:0000006	76.17	gold quality
ganglionic eminence	UBERON:0004023	75.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.59	gold quality
ventricular zone	UBERON:0003053	71.07	gold quality
vermiform appendix	UBERON:0001154	69.18	gold quality
caecum	UBERON:0001153	62.93	gold quality
lymph node	UBERON:0000029	62.76	gold quality
prefrontal cortex	UBERON:0000451	62.61	gold quality
gall bladder	UBERON:0002110	58.88	gold quality
granulocyte	CL:0000094	58.11	gold quality
rectum	UBERON:0001052	58.01	gold quality
smooth muscle tissue	UBERON:0001135	57.46	gold quality
epithelium of nasopharynx	UBERON:0001951	57.44	gold quality
amniotic fluid	UBERON:0000173	57.38	silver quality
calcaneal tendon	UBERON:0003701	57.21	gold quality
lower lobe of lung	UBERON:0008949	57.10	silver quality
spleen	UBERON:0002106	56.61	gold quality
cerebellar cortex	UBERON:0002129	56.49	gold quality
cerebellar hemisphere	UBERON:0002245	56.18	gold quality
anterior cingulate cortex	UBERON:0009835	56.02	gold quality
cerebellum	UBERON:0002037	55.62	gold quality
hypothalamus	UBERON:0001898	54.95	gold quality
neocortex	UBERON:0001950	54.90	gold quality
colonic epithelium	UBERON:0000397	54.89	gold quality
frontal cortex	UBERON:0001870	54.32	gold quality
right hemisphere of cerebellum	UBERON:0014890	53.87	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.59

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

84 targeting RAB39A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489

Literature-anchored findings (GeneRIF, showing 4)

• Results show that Rab39a interacts with caspase-1 and suggest that Rab39a functions as a trafficking adaptor linking caspase-1 to IL-1beta secretion. (PMID:19833722)
• our findings indicate that Rab39a favours chlamydial replication and infectivity. This is the first report showing that a late endocytic Rab GTPase is involved in chlamydial infection development. (PMID:26163492)
• C9ORF72 causes suboptimal autophagy (PMID:27494456)
• Molecular pathways regulated by RAB39A are transcriptionally maintained by the formation of molecular complex with RXRB, NCOR and HDAC that also contribute to cancer stemness. (PMID:29648608)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rab42a	ENSDARG00000034215
danio_rerio		ENSDARG00000102580
mus_musculus	Rab39	ENSMUSG00000055069
rattus_norvegicus	Rab39a	ENSRNOG00000063146

Paralogs (68): RAB27B (ENSG00000041353), RAB27A (ENSG00000069974), RAB7A (ENSG00000075785), RABL2B (ENSG00000079974), RAB21 (ENSG00000080371), RAB10 (ENSG00000084733), RAB18 (ENSG00000099246), RAB36 (ENSG00000100228), IFT27 (ENSG00000100360), RAB40AL (ENSG00000102128), RAB11A (ENSG00000103769), RAB2A (ENSG00000104388), RAB3D (ENSG00000105514), RAB3A (ENSG00000105649), RAB5C (ENSG00000108774), RAB34 (ENSG00000109113), RAB5B (ENSG00000111540), RAB35 (ENSG00000111737), RAB23 (ENSG00000112210), DNAJC27 (ENSG00000115137), RAB29 (ENSG00000117280), RAB32 (ENSG00000118508), RAB14 (ENSG00000119396), RAB9B (ENSG00000123570), RAB9A (ENSG00000123595), RAB38 (ENSG00000123892), RAB22A (ENSG00000124209), RAB17 (ENSG00000124839), RAB2B (ENSG00000129472), RAB25 (ENSG00000132698), RAB33A (ENSG00000134594), RAB30 (ENSG00000137502), RAB1A (ENSG00000138069), RAB20 (ENSG00000139832), RAB15 (ENSG00000139998), RAB40B (ENSG00000141542), RAB13 (ENSG00000143545), RABL2A (ENSG00000144134), RAB5A (ENSG00000144566), RAB19 (ENSG00000146955)

Protein

Protein identifiers

Ras-related protein Rab-39A — Q14964 (reviewed: Q14964)

All UniProt accessions (1): Q14964

UniProt curated annotations — full annotation on UniProt →

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. RAB39A regulates autophagosome-lysosome fusion via recruitment of the HOPS endosomal tethering complex onto lysosomes; this process involves lysosomal RAB39A and autophagosomal RAB2A recruitment of HOPS subcomplexes VPS41-VPS16-VPS18-VPS33A and VPS39-VPS11, respectively, which assemble into a functional complex to mediate membrane tethering and SNAREs-driven membrane fusion. Also negatively regulates lipopolysaccharide (LPS)-induced autophagosome formation in macrophages, possibly by implicating PI3K. Promotes the delivery of MHC-I molecules from the ER to phagosomes and the generation of peptide-loaded MHC-I complexes in phagosomes, thus enhancing antigen cross-presentation by dendritic cells. Plays a role in the maturation and acidification of phagosomes that engulf pathogens, such as S.aureus and M.tuberculosis. Plays a role in the fusion of phagosomes with lysosomes. May be involved in multiple neurite formation.

Subunit / interactions. Interacts (GDP-bound) with C9orf72; C9orf72 acts as a GEF for RAB39A. Interacts (GTP-bound) with HOPS complex components VPS39 and VPS41, and STX17; interaction between HOPS components and RAB39A contributes to obtaining a functional HOPS complex that promotes membrane fusion driven by STX17-SNAP29-VAMP8. Interacts with BECN1. Probably associates with the PI3K (PI3KC3/PI3K-III/class III phosphatidylinositol 3-kinase) complex. Interacts with UACA. Interacts with isoform a of RASSF1. Does not interact with isoform c of RASSF1.

Subcellular location. Cell membrane. Cytoplasmic vesicle. Phagosome membrane. Lysosome membrane. Autolysosome membrane.

Post-translational modifications. Prenylated. Prenylation is required for association with cellular membranes.

Activity regulation. Regulated by guanine nucleotide exchange factors (GEFs) including c9Orf72, which promote the exchange of bound GDP for free GTP. Regulated by GTPase activating proteins (GAPs) which increase the GTP hydrolysis activity. Inhibited by GDP dissociation inhibitors (GDIs).

Domain organisation. Switch I, switch II and the interswitch regions are characteristic of Rab GTPases and mediate the interactions with Rab downstream effectors. The switch regions undergo conformational changes upon nucleotide binding which drive interaction with specific sets of effector proteins, with most effectors only binding to GTP-bound Rab.

Similarity. Belongs to the small GTPase superfamily. Rab family.

RefSeq proteins (1): NP_059986* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001806	Small_GTPase	Family
IPR005225	Small_GTP-bd	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR041818	Rab39	Family
IPR050209	Rab_GTPases_membrane_traffic	Family

Pfam: PF00071

Catalyzed reactions (Rhea), 1 shown:

• GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)

UniProt features (31 total): binding site 15, mutagenesis site 5, sequence conflict 5, region of interest 2, lipid moiety-binding region 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q14964-F1	86.58	0.69

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (15): 44; 68; 71; 127; 128; 130; 158; 159; 17; 20; 21; 22 …

Post-translational modifications (3): 217, 215, 217

Mutagenesis-validated functional residues (5):

Position	Phenotype
22	constitutively inactive (gdp-bound) mutant. loss of localization to autolysosomes, decreased interaction with vps39 and
34–41	disrupts interaction with becn1.
72	constitutively active (gtp-bound) mutant. no change in subcellular localization under autophagy-induced conditions.
215	non-prenylatable mutant; when associated with a-217. loss of localization to autolysosomes and impaired autophagic flux
217	non-prenylatable mutant; when associated with a-215. loss of localization to autolysosomes and impaired autophagic flux

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6811438	Intra-Golgi traffic
R-HSA-8873719	RAB geranylgeranylation
R-HSA-8876198	RAB GEFs exchange GTP for GDP on RABs

MSigDB gene sets: 166 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, GOBP_VACUOLE_ORGANIZATION, GOCC_VACUOLAR_MEMBRANE, GOBP_VESICLE_ORGANIZATION, chr11q22, GOBP_MEMBRANE_FUSION, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_MACROAUTOPHAGY, GOBP_PHAGOLYSOSOME_ASSEMBLY, GOBP_PHAGOSOME_MATURATION, GOBP_ORGANELLE_MEMBRANE_FUSION, GOBP_PHAGOSOME_ACIDIFICATION, GOBP_ORGANELLE_ASSEMBLY, GOBP_REGULATION_OF_PH

GO Biological Process (7): protein transport (GO:0015031), vesicle-mediated transport (GO:0016192), Rab protein signal transduction (GO:0032482), autophagosome-lysosome fusion (GO:0061909), phagosome acidification (GO:0090383), phagosome-lysosome fusion (GO:0090385), autophagy (GO:0006914)

GO Molecular Function (7): GTPase activity (GO:0003924), G protein activity (GO:0003925), GTP binding (GO:0005525), metal ion binding (GO:0046872), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (11): Golgi membrane (GO:0000139), lysosomal membrane (GO:0005765), cytosol (GO:0005829), plasma membrane (GO:0005886), phagocytic vesicle membrane (GO:0030670), late endosome membrane (GO:0031902), phagocytic vesicle (GO:0045335), autolysosome membrane (GO:0120281), lysosome (GO:0005764), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Intra-Golgi and retrograde Golgi-to-ER traffic	1
Post-translational protein modification	1
Rab regulation of trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	2
vesicle fusion	2
cytoplasm	2
cellular anatomical structure	2
intracellular protein localization	1
establishment of protein localization	1
cellular process	1
small GTPase-mediated signal transduction	1
macroautophagy	1
intracellular pH reduction	1
phagosome maturation	1
phagolysosome assembly	1
catabolic process	1
transmembrane transport	1
process utilizing autophagic mechanism	1
ribonucleoside triphosphate phosphatase activity	1
GTPase activity	1
molecular function regulator activity	1
guanyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
cation binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
catalytic activity	1
Golgi apparatus	1
bounding membrane of organelle	1
lysosome	1
lytic vacuole membrane	1
membrane	1
cell periphery	1
endocytic vesicle membrane	1
phagocytic vesicle	1
late endosome	1
endosome membrane	1
endocytic vesicle	1
lysosomal membrane	1
autolysosome	1
lytic vacuole	1
intracellular vesicle	1

Protein interactions and networks

STRING

1375 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RAB39A	CWF19L2	Q2TBE0	611
RAB39A	CASP1	P29466	511
RAB39A	KIAA0513	O60268	474
RAB39A	CEP170B	Q9Y4F5	462
RAB39A	SLC35F2	Q8IXU6	457
RAB39A	NOL10	Q9BSC4	455
RAB39A	RABGGTA	Q92696	450
RAB39A	RAB3GAP1	Q15042	441
RAB39A	RXRB	P28702	438
RAB39A	RAB3IP	Q96QF0	430
RAB39A	RAB19	A4D1S5	415
RAB39A	SEC22B	O75396	412
RAB39A	RAB4A	P20338	411
RAB39A	RPRD2	Q5VT52	401
RAB39A	VAMP7	P51809	393

IntAct

50 interactions, top by confidence:

A	B	Type	Score
GOLGA2	RAB39A	psi-mi:“MI:0915”(physical association)	0.720
RAB39A	BLZF1	psi-mi:“MI:0915”(physical association)	0.720
RAB39A	GOLGA2	psi-mi:“MI:0915”(physical association)	0.720
RAB8A	WDR91	psi-mi:“MI:0914”(association)	0.600
RAB10	RAB39A	psi-mi:“MI:0915”(physical association)	0.560
RAB39A	GORASP2	psi-mi:“MI:0915”(physical association)	0.560
RAB12	CHM	psi-mi:“MI:0914”(association)	0.530
RAB39A	BECN1	psi-mi:“MI:0915”(physical association)	0.520
BECN1	RAB39A	psi-mi:“MI:0915”(physical association)	0.520
GYP1	RAB39A	psi-mi:“MI:0407”(direct interaction)	0.440
	RAB39A	psi-mi:“MI:0883”(gtpase reaction)	0.440
RAB39A	PIK3C3	psi-mi:“MI:0915”(physical association)	0.400
RAB39A	UVRAG	psi-mi:“MI:0915”(physical association)	0.400
RAB39A	ATG14	psi-mi:“MI:0915”(physical association)	0.400
RAB39A	RAB14	psi-mi:“MI:0915”(physical association)	0.400
RAB39A	NOL6	psi-mi:“MI:0915”(physical association)	0.400
	TK2	psi-mi:“MI:0915”(physical association)	0.400
RAB10	RAB19	psi-mi:“MI:0914”(association)	0.350
PB2		psi-mi:“MI:0914”(association)	0.350
	TSPO	psi-mi:“MI:0914”(association)	0.350
CD177	MYO1G	psi-mi:“MI:0914”(association)	0.350

BioGRID (63): RAB39A (Two-hybrid), RAB39A (Two-hybrid), RAB39A (Affinity Capture-MS), RAB39A (Affinity Capture-MS), RAB39A (Affinity Capture-MS), RAB39A (Affinity Capture-MS), RAB39A (Affinity Capture-Western), RAB39A (Affinity Capture-MS), RAB39A (Affinity Capture-MS), RAB39A (Affinity Capture-MS), RAB39A (Two-hybrid), RAB39A (Two-hybrid), RAB39A (Two-hybrid), RAB39A (Affinity Capture-MS), RAB39A (Proximity Label-MS)

ESM2 similar proteins: C8VQY7, G4MYS1, H9BW96, I1RMF2, O04157, O24461, O76742, O94655, O97572, P09527, P11023, P18067, P20336, P24408, P31022, P32939, P36411, P36864, P51149, P51150, P51151, P63011, P63012, P93267, Q06AU3, Q14964, Q39573, Q3T0F5, Q40787, Q41640, Q43463, Q4LE85, Q4R4R9, Q53B90, Q5R4W9, Q5R9Y4, Q8BHD0, Q8BHH2, Q8CG50, Q948K8

Diamond homologs: A4IHM6, F1PTE3, F4KFD8, O13876, O23657, O49841, P35286, P51153, P51157, P51158, P51159, Q14964, Q17QU4, Q18969, Q32LJ6, Q3SWY9, Q58DS5, Q5HYI8, Q5KTJ6, Q5RFI2, Q5UQ27, Q5ZKR4, Q6GPS4, Q6TNS7, Q7T3A4, Q7Z6P3, Q8BHC1, Q8BHD0, Q8N4Z0, Q948K8, Q96DA2, Q99KL7, Q9C5J9, Q9D4V7, Q9DD03, Q9SJ11, A5D7F5, A8HN58, E2RQ15, M0RC99

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 40 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
RAB geranylgeranylation	6	33.5×	2e-06
RAB GEFs exchange GTP for GDP on RABs	5	20.0×	1e-04
Macroautophagy	5	18.6×	1e-04

GO biological processes:

GO term	Partners	Fold	FDR
autophagosome maturation	5	50.1×	8e-06
autophagosome assembly	5	32.1×	4e-05
autophagy	6	18.9×	4e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

15 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	10
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

378 predictions. Top by Δscore:

Variant	Effect	Δscore
11:107928791:TTC:T	donor_gain	1.0000
11:107928792:TCAGG:T	donor_loss	1.0000
11:107928793:CAGGT:C	donor_loss	1.0000
11:107928794:AGGT:A	donor_loss	1.0000
11:107928795:GGT:G	donor_loss	1.0000
11:107928797:T:A	donor_loss	1.0000
11:107961944:A:AG	acceptor_gain	1.0000
11:107961945:G:GG	acceptor_gain	1.0000
11:107961945:GAT:G	acceptor_gain	1.0000
11:107961945:GATCA:G	acceptor_gain	1.0000
11:107961937:A:AG	acceptor_gain	0.9900
11:107961938:T:G	acceptor_gain	0.9900
11:107961940:TTTCA:T	acceptor_loss	0.9900
11:107961941:TTCA:T	acceptor_loss	0.9900
11:107961942:TCA:T	acceptor_loss	0.9900
11:107961943:CAGAT:C	acceptor_loss	0.9900
11:107961945:GA:G	acceptor_gain	0.9900
11:107961945:GATC:G	acceptor_gain	0.9900
11:107928796:G:GG	donor_gain	0.9800
11:107928758:C:G	donor_gain	0.9600
11:107942199:A:T	acceptor_gain	0.9500
11:107960270:A:AG	acceptor_gain	0.9400
11:107960271:G:GG	acceptor_gain	0.9400
11:107928786:A:T	donor_gain	0.9100
11:107928793:CAG:C	donor_gain	0.9000
11:107928745:C:T	donor_gain	0.8700
11:107960934:G:GT	acceptor_gain	0.8400
11:107928628:C:T	donor_gain	0.8200
11:107954542:AAAC:A	donor_gain	0.8200
11:107954543:AACA:A	donor_gain	0.8200

AlphaMissense

1406 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:107928771:A:C	D68A	0.999
11:107962101:A:T	K128I	0.999
11:107928630:A:T	K21M	0.998
11:107928631:G:C	K21N	0.998
11:107928631:G:T	K21N	0.998
11:107928767:T:A	W67R	0.998
11:107928767:T:C	W67R	0.998
11:107928771:A:T	D68V	0.998
11:107928772:C:A	D68E	0.998
11:107928772:C:G	D68E	0.998
11:107928791:T:C	F75L	0.998
11:107928793:C:A	F75L	0.998
11:107928793:C:G	F75L	0.998
11:107961995:T:C	F93L	0.998
11:107961997:T:A	F93L	0.998
11:107961997:T:G	F93L	0.998
11:107928629:A:C	K21Q	0.997
11:107928770:G:C	D68H	0.997
11:107928771:A:G	D68G	0.997
11:107962102:A:C	K128N	0.997
11:107962102:A:T	K128N	0.997
11:107962128:T:A	V137D	0.997
11:107928612:G:A	G15E	0.996
11:107928612:G:T	G15V	0.996
11:107928627:G:A	G20D	0.996
11:107928627:G:T	G20V	0.996
11:107928713:T:C	F49L	0.996
11:107928715:C:A	F49L	0.996
11:107928715:C:G	F49L	0.996
11:107928759:T:C	L64P	0.996

dbSNP variants (sampled 300 via entrez): RS1000124179 (11:107934856 G>A), RS1000384235 (11:107941604 C>T), RS1000651046 (11:107955616 A>G,T), RS1000798793 (11:107931634 G>A), RS1000845442 (11:107957818 T>A), RS1000902396 (11:107950895 G>A,T), RS1000933218 (11:107951324 C>G,T), RS1001159015 (11:107940973 GA>G,GAA,GAAA), RS1001232054 (11:107945317 A>C), RS1001276026 (11:107958120 G>A,T), RS1001341033 (11:107935526 C>T), RS1001410893 (11:107930832 G>A), RS1001442909 (11:107941194 G>A), RS1001582511 (11:107962519 G>A,C), RS1001627625 (11:107961488 A>G)

Disease associations

OMIM: gene MIM:619558 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067093 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.89	Kd	12.9	nM	CHEMBL5653589
7.89	ED50	12.9	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149175: Binding affinity to human RAB39A incubated for 45 mins by Kinobead based pull down assay	kd	0.0129	uM

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sotorasib	decreases expression, affects cotreatment	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
trametinib	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
theaflavin-3,3’-digallate	affects expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Acrylamide	increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652217	Binding	Binding affinity to human RAB39A incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.