RAB20

gene
On this page

Also known as FLJ20429

Summary

RAB20 (RAB20, member RAS oncogene family, HGNC:18260) is a protein-coding gene on chromosome 13q34, encoding Ras-related protein Rab-20 (Q9NX57). 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 GTPase activity. Involved in phagosome acidification and phagosome-lysosome fusion. Located in Golgi apparatus and phagocytic vesicle.

Source: NCBI Gene 55647 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 42 total
  • MANE Select transcript: NM_017817

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18260
Approved symbolRAB20
NameRAB20, member RAS oncogene family
Location13q34
Locus typegene with protein product
StatusApproved
AliasesFLJ20429
Ensembl geneENSG00000139832
Ensembl biotypeprotein_coding
Entrez55647

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000267328, ENST00000907762

RefSeq mRNA: 1 — MANE Select: NM_017817 NM_017817

CCDS: CCDS9512

Canonical transcript exons

ENST00000267328 — 2 exons

ExonStartEnd
ENSE00000940346110561348110561722
ENSE00000940347110523066110524197

Expression profiles

Bgee: expression breadth ubiquitous, 232 present calls, max score 98.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.4905 / max 271.5945, expressed in 1325 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
13825512.49051325

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065598.64gold quality
oocyteCL:000002396.16gold quality
pancreatic ductal cellCL:000207995.83gold quality
mucosa of transverse colonUBERON:000499192.12gold quality
right adrenal gland cortexUBERON:003582791.65gold quality
left adrenal gland cortexUBERON:003582591.38gold quality
left adrenal glandUBERON:000123491.05gold quality
right adrenal glandUBERON:000123390.80gold quality
spleenUBERON:000210690.80gold quality
nephron tubuleUBERON:000123190.38gold quality
adrenal tissueUBERON:001830390.37gold quality
adrenal glandUBERON:000236990.12gold quality
adrenal cortexUBERON:000123590.00gold quality
popliteal arteryUBERON:000225089.75gold quality
tibial arteryUBERON:000761089.75gold quality
monocyteCL:000057689.56gold quality
mononuclear cellCL:000084289.56gold quality
ileal mucosaUBERON:000033189.55gold quality
upper lobe of left lungUBERON:000895289.54gold quality
body of stomachUBERON:000116189.49gold quality
upper lobe of lungUBERON:000894889.43gold quality
lower lobe of lungUBERON:000894989.41silver quality
right lungUBERON:000216789.24gold quality
leukocyteCL:000073888.92gold quality
right lobe of liverUBERON:000111488.84gold quality
left coronary arteryUBERON:000162688.69gold quality
metanephric glomerulusUBERON:000473688.01gold quality
aortaUBERON:000094787.91gold quality
omental fat padUBERON:001041487.73gold quality
peritoneumUBERON:000235887.61gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SP1

miRNA regulators (miRDB)

25 targeting RAB20, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3646100.0073.565283
HSA-MIR-56899.9869.862084
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-7153-5P99.9468.891006
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-129999.7771.242389
HSA-MIR-442299.7272.072908
HSA-MIR-3158-5P99.6567.511763
HSA-MIR-875-3P99.6369.472548
HSA-MIR-302B-5P99.5069.491857
HSA-MIR-302D-5P99.5069.341863
HSA-MIR-520E-5P99.2768.901513
HSA-MIR-607199.1667.771780
HSA-MIR-510099.1167.521098
HSA-MIR-877-3P99.0968.101637
HSA-MIR-475198.8064.95525
HSA-MIR-502-5P98.7766.51906
HSA-MIR-6881-3P98.0468.241777
HSA-MIR-425797.8668.051190
HSA-MIR-6772-3P97.0465.89784
HSA-MIR-444897.0466.22752
HSA-MIR-6750-3P96.7967.50740
HSA-MIR-624-5P96.0068.88728
HSA-MIR-103B95.5166.85441

Literature-anchored findings (GeneRIF, showing 6)

  • Regulates connexin 43 intracellular transport. (PMID:18649179)
  • TdIF1 associates with the RAB20 promoter, and RAB20 gene transcription is reduced in TdIF1-knocked-down cells, suggesting that TdIF1 stimulates RAB20 gene transcription. (PMID:23874396)
  • Rab20 is specifically and significantly upregulated in the sputum of human patients with active tuberculosis. (PMID:28494243)
  • Regulation of Small GTPase Rab20 by Ikaros in B-Cell Acute Lymphoblastic Leukemia. (PMID:32138279)
  • Low oxygen saturation during sleep reduces CD1D and RAB20 expressions that are reversed by CPAP therapy. (PMID:32512511)
  • TPI1-reduced extracellular vesicles mediated by Rab20 downregulation promotes aerobic glycolysis to drive hepatocarcinogenesis. (PMID:34401050)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriorab20ENSDARG00000005049
mus_musculusRab20ENSMUSG00000031504
rattus_norvegicusRab20ENSRNOG00000023991
caenorhabditis_elegansWBGENE00016874

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), RAB15 (ENSG00000139998), RAB40B (ENSG00000141542), RAB13 (ENSG00000143545), RABL2A (ENSG00000144134), RAB5A (ENSG00000144566), RAB19 (ENSG00000146955), RAB41 (ENSG00000147127)

Protein

Protein identifiers

Ras-related protein Rab-20Q9NX57 (reviewed: Q9NX57)

All UniProt accessions (1): Q9NX57

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. RAB20 plays a role in apical endocytosis/recycling. 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.

Subcellular location. Golgi apparatus. Cytoplasmic vesicle. Phagosome. Phagosome membrane.

Tissue specificity. Low or absent expression in normal pancreas and stronger expression in 15 of 18 exocrine pancreatic adenocarcinomas (at protein level).

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 1, switch 2 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_060287* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001806Small_GTPaseFamily
IPR005225Small_GTP-bdDomain
IPR027417P-loop_NTPaseHomologous_superfamily
IPR041836Rab20Family

Pfam: PF00071

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (25 total): binding site 14, region of interest 2, lipid moiety-binding region 2, short sequence motif 2, compositionally biased region 2, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NX57-F187.020.72

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 (14): 19; 32; 36; 36; 55; 58; 113; 114; 116; 184; 185; 17

Post-translational modifications (2): 232, 233

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-8873719RAB geranylgeranylation

MSigDB gene sets: 284 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, GOBP_VACUOLE_ORGANIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_RESPONSE_TO_PEPTIDE, GOBP_VESICLE_ORGANIZATION, GOBP_MEMBRANE_FUSION, GOBP_VESICLE_MEDIATED_TRANSPORT, WIELAND_UP_BY_HBV_INFECTION, GOBP_PHAGOLYSOSOME_ASSEMBLY, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, FOSTER_TOLERANT_MACROPHAGE_DN, GOBP_PHAGOSOME_MATURATION, ROZANOV_MMP14_TARGETS_UP, GOBP_ORGANELLE_MEMBRANE_FUSION, chr13q34

GO Biological Process (6): intracellular protein transport (GO:0006886), endocytosis (GO:0006897), cellular response to type II interferon (GO:0071346), phagosome acidification (GO:0090383), phagosome-lysosome fusion (GO:0090385), protein transport (GO:0015031)

GO Molecular Function (6): GTPase activity (GO:0003924), G protein activity (GO:0003925), GTP binding (GO:0005525), metal ion binding (GO:0046872), nucleotide binding (GO:0000166), hydrolase activity (GO:0016787)

GO Cellular Component (9): early endosome (GO:0005769), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), endomembrane system (GO:0012505), endocytic vesicle (GO:0030139), phagocytic vesicle membrane (GO:0030670), phagocytic vesicle (GO:0045335), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Post-translational protein modification1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular protein localization2
cytoplasm2
cellular anatomical structure2
protein transport1
intracellular transport1
vesicle budding from membrane1
membrane invagination1
vesicle-mediated transport1
import into cell1
response to type II interferon1
cellular response to cytokine stimulus1
intracellular pH reduction1
phagosome maturation1
phagolysosome assembly1
vesicle fusion1
transport1
establishment of protein localization1
ribonucleoside triphosphate phosphatase activity1
GTPase activity1
molecular function regulator activity1
guanyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
cation binding1
nucleoside phosphate binding1
heterocyclic compound binding1
catalytic activity1
endosome1
endomembrane system1
intracellular membrane-bounded organelle1
membrane1
cell periphery1
vacuole1
plasma membrane1
cytoplasmic vesicle1
endocytic vesicle membrane1
phagocytic vesicle1
endocytic vesicle1
intracellular vesicle1

Protein interactions and networks

STRING

960 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RAB20RABGEF1Q9UJ41628
RAB20RAB5AP20339462
RAB20RIMKLAQ8IXN7437
RAB20RAB10P61026418
RAB20DNTTIP1Q9H147394
RAB20NAXDQ8IW45392
RAB20TMEM101Q96IK0372
RAB20GATAD1Q8WUU5355
RAB20CEBPZOSA8MTT3353
RAB20PEX12O00623350
RAB20SLCO5A1Q9H2Y9349
RAB20WNT11O96014349
RAB20PRR32B1ATL7316
RAB20OSBPL1AQ9BXW6306
RAB20TMEM223A0PJW6305

IntAct

14 interactions, top by confidence:

ABTypeScore
UNC119UNC119Bpsi-mi:“MI:0914”(association)0.640
RAB20CHMpsi-mi:“MI:0914”(association)0.530
RAB20psi-mi:“MI:0883”(gtpase reaction)0.440
virApsi-mi:“MI:0883”(gtpase reaction)0.440
HLA-Cpsi-mi:“MI:0914”(association)0.350
Npc1ESYT2psi-mi:“MI:0914”(association)0.350
RAB20BCL10psi-mi:“MI:0914”(association)0.350
MFSD11PLD2psi-mi:“MI:0914”(association)0.350
SLC27A5MEIOCpsi-mi:“MI:0914”(association)0.350
SLC39A11ESYT2psi-mi:“MI:0914”(association)0.350
SLC39A12ESYT2psi-mi:“MI:0914”(association)0.350
SV2BC15orf61psi-mi:“MI:0914”(association)0.350

BioGRID (27): RAB20 (Affinity Capture-RNA), RAB20 (Affinity Capture-MS), RAB20 (Affinity Capture-RNA), ANKRD13D (Affinity Capture-MS), TFCP2 (Affinity Capture-MS), RAP1GDS1 (Affinity Capture-MS), CHM (Affinity Capture-MS), CHML (Affinity Capture-MS), PGGT1B (Affinity Capture-MS), ALKBH1 (Affinity Capture-MS), MINA (Affinity Capture-MS), UBP1 (Affinity Capture-MS), SPATA20 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), RABGGTA (Affinity Capture-MS)

ESM2 similar proteins: A1DZY4, A6QP66, O35626, O35929, O88910, O88954, P0C0E4, P35295, P51157, P51158, P53667, P53668, P53669, P55040, P55041, P55043, P63032, P63033, Q06AU5, Q12829, Q13368, Q13637, Q3SWY9, Q5E9J3, Q5FVY2, Q5R541, Q5RFI2, Q6DGN0, Q6IMA3, Q6IMA7, Q6IMB1, Q6P0U3, Q6T310, Q8AVS6, Q8IYK8, Q8QFP8, Q8VEL9, Q8VHP8, Q8VHQ4, Q8WXH6

Diamond homologs: A4FV54, C4YL11, C8VQY7, M0RC99, O04157, O23657, O24461, O42819, O49841, O76173, O76742, O94655, P07560, P0CY30, P0CY31, P18066, P20339, P22127, P22128, P24409, P29687, P31582, P31583, P34142, P35278, P35280, P35282, P35285, P35292, P35295, P36411, P36586, P36864, P41924, P41925, P51147, P51148, P51153, P55258, P55745

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance40
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

679 predictions. Top by Δscore:

VariantEffectΔscore
13:110524193:CCGCC:Cacceptor_gain1.0000
13:110524194:CGCC:Cacceptor_gain1.0000
13:110524194:CGCCC:Cacceptor_gain1.0000
13:110524195:GCC:Gacceptor_gain1.0000
13:110524196:CC:Cacceptor_gain1.0000
13:110524196:CCC:Cacceptor_gain1.0000
13:110524197:CC:Cacceptor_gain1.0000
13:110524198:C:CAacceptor_loss1.0000
13:110524198:C:CCacceptor_gain1.0000
13:110524198:C:Tacceptor_gain1.0000
13:110524199:T:Cacceptor_loss1.0000
13:110524201:G:GCacceptor_gain1.0000
13:110561342:CCTCA:Cdonor_loss1.0000
13:110561343:CTCA:Cdonor_loss1.0000
13:110561344:TCA:Tdonor_loss1.0000
13:110561345:CA:Cdonor_loss1.0000
13:110561346:A:ATdonor_loss1.0000
13:110561347:C:CTdonor_loss1.0000
13:110524201:G:Cacceptor_gain0.9900
13:110540205:G:Cdonor_gain0.9900
13:110561347:CCTG:Cdonor_gain0.9900
13:110524195:GCCCT:Gacceptor_gain0.9700
13:110542754:C:CCacceptor_gain0.9700
13:110561346:A:ACdonor_gain0.9700
13:110561347:C:CCdonor_gain0.9700
13:110524196:CCCTG:Cacceptor_gain0.9600
13:110524198:CT:Cacceptor_gain0.9600
13:110524197:CCT:Cacceptor_gain0.9500
13:110524199:T:Gacceptor_gain0.9400
13:110534579:TTG:Tdonor_gain0.9400

AlphaMissense

1542 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
13:110524029:T:AK114I0.999
13:110524184:G:CF62L0.999
13:110524184:G:TF62L0.999
13:110524186:A:GF62L0.999
13:110561356:T:AD55V0.999
13:110561356:T:GD55A0.999
13:110524028:T:AK114N0.998
13:110524028:T:GK114N0.998
13:110561357:C:GD55H0.998
13:110561360:A:GW54R0.998
13:110561360:A:TW54R0.998
13:110523821:G:CS183R0.997
13:110523821:G:TS183R0.997
13:110523823:T:GS183R0.997
13:110561355:G:CD55E0.997
13:110561355:G:TD55E0.997
13:110561356:T:CD55G0.997
13:110561449:C:GR24P0.997
13:110561430:G:CF30L0.996
13:110561430:G:TF30L0.996
13:110561432:A:GF30L0.996
13:110561470:C:TG17E0.996
13:110561485:C:TG12E0.996
13:110561486:C:GG12R0.996
13:110561486:C:TG12R0.996
13:110523819:G:TA184D0.995
13:110524030:T:CK114E0.995
13:110524109:G:CS87R0.995
13:110524109:G:TS87R0.995
13:110524111:T:GS87R0.995

dbSNP variants (sampled 300 via entrez): RS1000102567 (13:110549434 G>A), RS1000259928 (13:110546102 A>C), RS1000362361 (13:110538691 G>C), RS1000392683 (13:110556167 A>C,T), RS1000484134 (13:110534084 G>A,T), RS1000606291 (13:110541887 A>T), RS1000737784 (13:110545722 G>A), RS1000765228 (13:110540062 T>C), RS1000775564 (13:110531015 T>C,G), RS1000818333 (13:110538975 G>T), RS1000846294 (13:110523848 G>A), RS1000857306 (13:110557067 G>A,C), RS1000876000 (13:110523508 C>A,T), RS1000916896 (13:110552998 G>A), RS1000951299 (13:110536169 G>A,C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST004253_3Accelerated cognitive decline after conversion of mild cognitive impairment to Alzheimer’s disease (Alzhiemer’s diagnosis trajectory interaction)2.000000e-06
GCST010653_23Thyroid stimulating hormone levels9.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007710cognitive decline measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, increases methylation9
trichostatin Aaffects cotreatment, increases expression3
Acetaminophendecreases expression, affects response to substance3
Benzo(a)pyrenedecreases expression, increases methylation, affects methylation3
mercuric bromideincreases expression, affects cotreatment2
entinostatincreases expression, affects cotreatment2
Vorinostataffects cotreatment, increases expression2
Panobinostataffects cotreatment, increases expression2
Phenylmercuric Acetateincreases expression, affects cotreatment2
p-Chloromercuribenzoic Acidincreases expression, affects cotreatment2
aristolochic acid Idecreases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, increases methylation1
glycidyl methacrylatedecreases expression1
sulforaphanedecreases expression1
zinc chloridedecreases reaction, increases expression1
sodium arsenitedecreases expression1
cobaltous chloridedecreases reaction, increases expression1
ferrous chloridedecreases expression1
aflatoxin B2decreases methylation1
1-nitropyrenedecreases expression1
di-n-butylphosphoric acidaffects expression1
Am 580increases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
abrinedecreases expression1
dorsomorphinincreases expression, affects cotreatment1
Rosiglitazoneincreases expression1
Sunitinibincreases expression1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B2D0Abcam HeLa RAB20 KOCancer cell lineFemale
CVCL_TI01HAP1 RAB20 (-) 1Cancer cell lineMale
CVCL_TI02HAP1 RAB20 (-) 2Cancer cell lineMale
CVCL_TI03HAP1 RAB20 (-) 3Cancer cell lineMale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.