RAB42

Summary

RAB42 (RAB42, member RAS oncogene family, HGNC:28702) is a protein-coding gene on chromosome 1p35.3, encoding Ras-related protein Rab-42 (Q8N4Z0). 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 GDP binding activity; GTP binding activity; and GTPase activity. Predicted to be located in membrane. Predicted to be active in plasma membrane.

Source: NCBI Gene 115273 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 35 total
• Phenotypes (HPO): 1
• MANE Select transcript: NM_001193532

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28702
Approved symbol	RAB42
Name	RAB42, member RAS oncogene family
Location	1p35.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC45806
Ensembl gene	ENSG00000188060
Ensembl biotype	protein_coding
Entrez	115273

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000373826, ENST00000465518

RefSeq mRNA: 2 — MANE Select: NM_001193532 NM_001193532, NM_152304

CCDS: CCDS325, CCDS85943

Canonical transcript exons

ENST00000465518 — 2 exons

Exon	Start	End
ENSE00001763496	28593694	28595449
ENSE00001897753	28592265	28592744

Expression profiles

Bgee: expression breadth ubiquitous, 130 present calls, max score 79.91.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1668 / max 5.5879, expressed in 70 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
1819	0.1668	70

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.91	gold quality
lymph node	UBERON:0000029	77.22	gold quality
placenta	UBERON:0001987	76.26	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	70.54	gold quality
ventricular zone	UBERON:0003053	70.54	gold quality
stromal cell of endometrium	CL:0002255	69.31	gold quality
gall bladder	UBERON:0002110	68.62	gold quality
smooth muscle tissue	UBERON:0001135	68.00	gold quality
spleen	UBERON:0002106	67.93	gold quality
subcutaneous adipose tissue	UBERON:0002190	67.55	gold quality
rectum	UBERON:0001052	67.29	gold quality
islet of Langerhans	UBERON:0000006	66.54	gold quality
duodenum	UBERON:0002114	66.44	gold quality
adipose tissue	UBERON:0001013	66.43	gold quality
vermiform appendix	UBERON:0001154	66.15	gold quality
mucosa of transverse colon	UBERON:0004991	66.10	gold quality
transverse colon	UBERON:0001157	65.71	gold quality
apex of heart	UBERON:0002098	65.36	gold quality
urinary bladder	UBERON:0001255	65.16	gold quality
thoracic mammary gland	UBERON:0005200	65.05	gold quality
omental fat pad	UBERON:0010414	65.04	gold quality
endometrium	UBERON:0001295	64.70	gold quality
ganglionic eminence	UBERON:0004023	64.27	gold quality
bone marrow cell	CL:0002092	64.03	silver quality
endocervix	UBERON:0000458	64.00	gold quality
ectocervix	UBERON:0012249	63.86	gold quality
right coronary artery	UBERON:0001625	63.64	gold quality
minor salivary gland	UBERON:0001830	62.84	gold quality
saliva-secreting gland	UBERON:0001044	62.80	gold quality
colonic epithelium	UBERON:0000397	62.35	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting RAB42, 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-6778-3P	99.96	67.29	2693
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-4676-3P	99.65	69.31	1733
HSA-MIR-892C-3P	99.65	69.38	1745
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-519D-5P	99.41	69.30	2057
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-6877-3P	98.98	65.83	560
HSA-MIR-6819-3P	98.95	65.57	572
HSA-MIR-619-5P	98.57	64.97	1988
HSA-MIR-6852-3P	98.54	67.60	1468
HSA-MIR-4726-3P	98.49	63.89	1385
HSA-MIR-3159	97.94	66.79	1098
HSA-MIR-6747-3P	97.73	64.84	1596
HSA-MIR-215-3P	97.02	68.01	1209
HSA-MIR-2355-3P	96.84	68.54	909
HSA-MIR-4529-5P	96.74	65.77	569

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rab42	ENSMUSG00000089687
rattus_norvegicus	Rab42	ENSRNOG00000063150

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-42 — Q8N4Z0 (reviewed: Q8N4Z0)

All UniProt accessions (1): Q8N4Z0

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. The physiological function of RAB42 remains undefined.

Subcellular location. Membrane.

Activity regulation. Regulated by guanine nucleotide exchange factors (GEFs) 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.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N4Z0-2	1	yes
Q8N4Z0-1	2

RefSeq proteins (2): NP_001180461, NP_689517 (=MANE)

Domains & families (InterPro)

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

Pfam: PF00071

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (17 total): binding site 13, lipid moiety-binding region 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N4Z0-F1	85.55	0.61

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 (13): 19; 130; 132; 160; 161; 21; 22; 23; 23; 46; 46; 70 …

Post-translational modifications (2): 216, 218

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-8873719	RAB geranylgeranylation

MSigDB gene sets: 53 (showing top): GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, chr1p35, GOMF_GTPASE_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, KRIEG_HYPOXIA_NOT_VIA_KDM3A, FORTSCHEGGER_PHF8_TARGETS_DN, REACTOME_RAB_GERANYLGERANYLATION, NFE2L2.V2, GSE14415_NATURAL_TREG_VS_FOXP3_KO_NATURAL_TREG_UP, ZSCAN2_TARGET_GENES, MIR7151_3P, MIR452_5P, MIR892C_3P

GO Biological Process (0):

GO Molecular Function (8): GTPase activity (GO:0003924), G protein activity (GO:0003925), GTP binding (GO:0005525), GDP binding (GO:0019003), metal ion binding (GO:0046872), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Post-translational protein modification	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
guanyl ribonucleotide binding	2
ribonucleoside triphosphate phosphatase activity	1
GTPase activity	1
molecular function regulator activity	1
purine ribonucleoside triphosphate binding	1
anion binding	1
cation binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
catalytic activity	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1041 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RAB42	TMEM61	Q8N0U2	479
RAB42	DYDC1	Q8WWB3	448
RAB42	KLHDC8A	Q8IYD2	443
RAB42	C16orf86	Q6ZW13	431
RAB42	TMEM71	Q6P5X7	420
RAB42	DYDC2	Q96IM9	417
RAB42	GPR179	Q6PRD1	385
RAB42	CCDC18	Q5T9S5	375
RAB42	CHM	P24386	374
RAB42	TRNAU1AP	Q9NX07	365
RAB42	PPP1R13B	Q96KQ4	357
RAB42	CHML	P26374	357
RAB42	DCAF17	Q5H9S7	343
RAB42	DCTN5	Q9BTE1	333
RAB42	SLC35F2	Q8IXU6	327

IntAct

1 interactions, top by confidence:

BioGRID (3): RAB42 (Two-hybrid), RAB42 (Positive Genetic), RAB42 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: E2RQ15, M0RC99, P10948, P18066, P20337, P20339, P24408, P35278, P35283, P35284, P35289, P35292, P46629, P51146, P51147, P51148, P57735, P59190, P61017, P61018, P61020, P61021, P61271, P97950, Q06AU6, Q0IIG7, Q0ILQ6, Q0PD08, Q14088, Q1RMR4, Q32NQ0, Q40520, Q53B90, Q58DS9, Q58DW6, Q5R4W9, Q5R7L7, Q5RBG1, Q5ZHW4, Q6IQ22

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, A4FV54, C4YL11, O04486, O18333

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1407 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:28593743:T:C	F95L	0.986
1:28593745:T:A	F95L	0.986
1:28593745:T:G	F95L	0.986
1:28592577:G:C	K22N	0.969
1:28592577:G:T	K22N	0.969
1:28592740:T:C	F77L	0.968
1:28592742:C:A	F77L	0.968
1:28592742:C:G	F77L	0.968
1:28593968:T:C	F170L	0.967
1:28593970:T:A	F170L	0.967
1:28593970:T:G	F170L	0.967
1:28592576:A:T	K22M	0.960
1:28592720:A:C	D70A	0.960
1:28593850:G:C	K130N	0.960
1:28593850:G:T	K130N	0.960
1:28592575:A:C	K22Q	0.959
1:28593903:C:A	A148D	0.959
1:28592719:G:C	D70H	0.958
1:28592720:A:T	D70V	0.956
1:28592539:T:C	F10L	0.954
1:28592541:T:A	F10L	0.954
1:28592541:T:G	F10L	0.954
1:28593990:T:A	I177N	0.953
1:28593876:T:A	V139D	0.952
1:28592721:C:A	D70E	0.951
1:28592721:C:G	D70E	0.951
1:28593765:C:T	S102F	0.951
1:28593840:T:A	V127D	0.951
1:28592576:A:C	K22T	0.949
1:28593710:T:C	F84L	0.946

dbSNP variants (sampled 300 via entrez): RS1000066869 (1:28592950 G>A), RS1000544409 (1:28594799 G>A), RS1000669088 (1:28591002 C>T), RS1001145277 (1:28590868 G>A,C,T), RS1001146342 (1:28596196 TCAGA>T), RS1001994341 (1:28591368 G>A,T), RS1002226585 (1:28596775 C>A,T), RS1003056118 (1:28592441 G>A), RS1003226400 (1:28593508 G>A,C,T), RS1004136639 (1:28591402 C>T), RS1004723956 (1:28591864 A>G), RS1005015963 (1:28595571 C>T), RS1005612308 (1:28590493 T>A), RS1006044790 (1:28597065 G>A), RS1006366762 (1:28596968 A>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:209850

GenCC curated gene-disease

Mondo (1): autism (MONDO:0005260)

Orphanet (0):

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0000717	Autism

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D001321	Autistic Disorder	F03.625.164.113.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
sulforaphane	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
nickel sulfate	decreases expression	1
coumarin	increases phosphorylation	1
resorcinol	increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects response to substance	1
CGP 52608	affects binding, increases reaction	1
entinostat	increases expression	1
K 7174	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Cadmium	decreases expression	1
Caffeine	decreases phosphorylation	1
Cisplatin	affects cotreatment, decreases expression	1
Hydrogen Peroxide	affects expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Quercetin	decreases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
Cyclosporine	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00211796	PHASE4	COMPLETED	Divalproex Sodium ER in Adult Autism
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT00409747	PHASE4	COMPLETED	Minocycline to Treat Childhood Regressive Autism
NCT00576732	PHASE4	COMPLETED	A Study of the Effectiveness and Safety of Two Doses of Risperidone in the Treatment of Children and Adolescents With Autistic Disorder
NCT00844753	PHASE4	COMPLETED	Atomoxetine, Placebo and Parent Management Training in Autism
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01098383	PHASE4	UNKNOWN	Treatment With Acetyl-Choline Esterase Inhibitors in Children With Autism Spectrum Disorders
NCT01333865	PHASE4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	PHASE4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	PHASE4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02069977	PHASE4	UNKNOWN	Study to Evaluate the Efficacy and Safety of Aripiprazole
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02199925	PHASE4	UNKNOWN	An Open-Label Study to Evaluate the Efficacy of High-Dose Gammaplex in Children on the Autism Spectrum
NCT02235467	PHASE4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02255565	PHASE4	COMPLETED	Dose Response Effects of Quillivant XR in Children With ADHD and Autism: A Pilot Study
NCT02940574	PHASE4	COMPLETED	Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629	PHASE4	COMPLETED	Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646	PHASE4	COMPLETED	Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431	PHASE4	COMPLETED	Improving Driving in Young People With Autism Spectrum Disorders
NCT03757585	PHASE4	COMPLETED	Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353	PHASE4	COMPLETED	Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656	PHASE4	COMPLETED	Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245	PHASE4	UNKNOWN	Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339	PHASE4	RECRUITING	AWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052	PHASE4	TERMINATED	A Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665	PHASE4	RECRUITING	The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697	PHASE4	COMPLETED	Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804	PHASE4	COMPLETED	Pilot RCT Using Homeopathic Medicines in ASD
NCT07439042	PHASE4	NOT_YET_RECRUITING	Buspirone for Anxiety in Autistic Youth
NCT00036231	PHASE3	TERMINATED	Synthetic Human Secretin in Children With Autism and Gastrointestinal Dysfunction
NCT00036244	PHASE3	COMPLETED	Synthetic Human Secretin in Children With Autism
NCT00065884	PHASE3	UNKNOWN	Valproate Response in Aggressive Autistic Adolescents
NCT00065962	PHASE3	COMPLETED	Secretin for the Treatment of Autism
NCT00252603	PHASE3	COMPLETED	Galantamine Versus Placebo in Childhood Autism
NCT00346736	PHASE3	COMPLETED	Use of Acupuncture In Children With Autistic Spectrum Disorder
NCT00352248	PHASE3	COMPLETED	Randomized Controlled Trial of Acupuncture Versus Sham Acupuncture in Autistic Spectrum Disorder
NCT00352352	PHASE3	COMPLETED	Use of Acupuncture In Children With Autistic Spectrum Disorder
NCT00355329	PHASE3	COMPLETED	Randomized Control Trial of Using Tongue Acupuncture in Autistic Spectrum Disorder Using PET Scan for Clinical Correlation
NCT00498173	PHASE3	COMPLETED	Effectiveness of Atomoxetine in Treating ADHD Symptoms in Children and Adolescents With Autism
NCT00541346	PHASE3	COMPLETED	A Pilot Study of Daytrana TM in Children With Autism Co-Morbid for Attention Deficit Hyperactivity Disorder (ADHD) Symptoms