RAB41

Summary

RAB41 (RAB41, member RAS oncogene family, HGNC:18293) is a protein-coding gene on chromosome Xq13.1, encoding Ras-related protein Rab-41 (Q5JT25). The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes.

This gene encodes a small GTP-binding protein that belongs to the largest family within the Ras superfamily. These proteins function as regulators of membrane trafficking. They cycle between inactive GDP-bound and activated GTP-bound states, which is controlled by GTP hydrolysis-activating proteins (GAPs). This family member can be activated by the GAP protein RN-Tre, and it is localized to the Golgi complex.

Source: NCBI Gene 347517 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 55 total
• MANE Select transcript: NM_001363807

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18293
Approved symbol	RAB41
Name	RAB41, member RAS oncogene family
Location	Xq13.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000147127
Ensembl biotype	protein_coding
Entrez	347517

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000276066, ENST00000374473, ENST00000509895

RefSeq mRNA: 2 — MANE Select: NM_001363807 NM_001032726, NM_001363807

CCDS: CCDS35322, CCDS87756

Canonical transcript exons

ENST00000374473 — 8 exons

Exon	Start	End
ENSE00000978849	70283513	70283624
ENSE00001154997	70283950	70284043
ENSE00001162597	70282533	70282591
ENSE00001463608	70284588	70285002
ENSE00001463610	70284266	70284329
ENSE00001463613	70282172	70282341
ENSE00001617505	70282802	70282855
ENSE00001729273	70283268	70283373

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 88.54.

Top tissues by expression

134 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	88.54	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.92	gold quality
substantia nigra	UBERON:0002038	75.04	gold quality
amygdala	UBERON:0001876	74.58	gold quality
temporal lobe	UBERON:0001871	74.42	gold quality
caudate nucleus	UBERON:0001873	74.36	gold quality
putamen	UBERON:0001874	74.08	gold quality
hypothalamus	UBERON:0001898	73.57	gold quality
nucleus accumbens	UBERON:0001882	73.24	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	73.13	gold quality
anterior cingulate cortex	UBERON:0009835	73.06	gold quality
Ammon’s horn	UBERON:0001954	72.31	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	72.26	gold quality
right frontal lobe	UBERON:0002810	71.76	gold quality
cerebral cortex	UBERON:0000956	71.35	gold quality
Brodmann (1909) area 9	UBERON:0013540	71.26	gold quality
brain	UBERON:0000955	70.37	gold quality
frontal cortex	UBERON:0001870	70.24	gold quality
prefrontal cortex	UBERON:0000451	69.55	gold quality
primary visual cortex	UBERON:0002436	69.29	gold quality
right testis	UBERON:0004534	68.86	gold quality
testis	UBERON:0000473	68.48	gold quality
left testis	UBERON:0004533	67.45	gold quality
cerebellar hemisphere	UBERON:0002245	66.98	gold quality
cerebellar cortex	UBERON:0002129	66.96	gold quality
cerebellum	UBERON:0002037	66.87	gold quality
right hemisphere of cerebellum	UBERON:0014890	66.75	gold quality
superior frontal gyrus	UBERON:0002661	65.64	gold quality
ganglionic eminence	UBERON:0004023	65.31	gold quality
smooth muscle tissue	UBERON:0001135	64.97	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	27.49
E-GEOD-137537	yes	4.21
E-ANND-3	yes	2.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting RAB41, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-7151-5P	99.37	67.82	613
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-4434	99.10	67.01	1984
HSA-MIR-5703	99.10	67.09	2053
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-519A-2-5P	98.78	71.74	1401
HSA-MIR-520B-5P	98.78	71.74	1401
HSA-MIR-219A-2-3P	98.62	68.78	797
HSA-MIR-4726-3P	98.49	63.89	1385
HSA-MIR-6804-5P	98.39	65.77	1084
HSA-MIR-4684-5P	98.29	67.99	1650
HSA-MIR-582-3P	96.69	67.38	1019
HSA-MIR-3135A	96.41	65.30	494
HSA-MIR-12115	94.19	66.37	738
HSA-MIR-3677-5P	93.16	64.62	393

Literature-anchored findings (GeneRIF, showing 3)

• distinctive Rab41 effects on Golgi organization, ER-to-Golgi trafficking and cell growth (PMID:23936529)
• Streptococcus pneumoniae is entrapped by selective autophagy in pneumolysin- and ubiquitin-p62-LC3 cargo-dependent manners. Streptococcus pneumoniae-containing autophagic vesicles (PcAV) were formed only in the presence of Rab41-positive intact Golgi apparatuses. Nedd4-1 was recruited to PcAV which played a pivotal role in K63-linked polyubiquitin chain (K63Ub) generation on PcAV and elimination of intracellular bacteria. (PMID:29582580)
• Rab41-mediated ESCRT machinery repairs membrane rupture by a bacterial toxin in xenophagy. (PMID:37802980)

Cross-species orthologs

0 orthologs

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-41 — Q5JT25 (reviewed: Q5JT25)

All UniProt accessions (2): Q5JT25, D6REW8

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. RAB41 is required for normal Golgi ribbon organization and ER-to-Golgi trafficking.

Subcellular location. Cytoplasm.

Tissue specificity. Widely expressed in brain, testis, lung, heart, ovary, colon, kidney, uterus and spleen but not in liver.

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 drives 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?
Q5JT25-1	1	yes
Q5JT25-2	2

RefSeq proteins (2): NP_001027898, NP_001350736* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001806	Small_GTPase	Family
IPR005225	Small_GTP-bd	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR050227	Rab	Family

Pfam: PF00071

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (22 total): binding site 17, region of interest 2, chain 1, lipid moiety-binding region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JT25-F1	80.23	0.62

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 (17): 63; 63; 86; 89; 144; 145; 147; 174; 175; 176; 41; 42 …

Post-translational modifications (1): 222

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-6811438	Intra-Golgi traffic
R-HSA-8873719	RAB geranylgeranylation

MSigDB gene sets: 38 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_INTRA_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOBP_PROTEIN_LOCALIZATION_TO_GOLGI_APPARATUS, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_RETROGRADE_TRANSPORT_ENDOSOME_TO_GOLGI, GOBP_LOCALIZATION_WITHIN_MEMBRANE, GOBP_CYTOSOLIC_TRANSPORT, GOMF_GTPASE_ACTIVITY, GOBP_GOLGI_VESICLE_TRANSPORT, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, chrXq13, GOBP_RETROGRADE_VESICLE_MEDIATED_TRANSPORT_GOLGI_TO_ENDOPLASMIC_RETICULUM

GO Biological Process (5): intracellular protein transport (GO:0006886), retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum (GO:0006890), intra-Golgi vesicle-mediated transport (GO:0006891), retrograde transport, endosome to Golgi (GO:0042147), protein localization to Golgi membrane (GO:1903292)

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 (6): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), cytosol (GO:0005829), plasma membrane (GO:0005886), endomembrane system (GO:0012505), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Intra-Golgi and retrograde Golgi-to-ER traffic	1
Post-translational protein modification	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
Golgi vesicle transport	2
cytoplasm	2
intracellular protein localization	1
protein transport	1
intracellular transport	1
intercellular transport	1
endosomal transport	1
cytosolic transport	1
protein localization to Golgi apparatus	1
protein localization to membrane	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
endomembrane system	1
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1
vacuole	1
plasma membrane	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

636 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RAB41	TBC1D20	Q96BZ9	290
RAB41	VPS45	Q9NRW7	272
RAB41	STX16	O14662	262
RAB41	ARL1	P40616	251
RAB41	VPS53	Q5VIR6	250
RAB41	VPS52	Q8N1B4	247
RAB41	TBC1D5	Q92609	247
RAB41	RGP1	Q92546	246
RAB41	TMEM11	P17152	243
RAB41	RABGEF1	Q9UJ41	236
RAB41	VPS54	Q9P1Q0	213
RAB41	GOLPH3L	Q9H4A5	209
RAB41	DENND5A	Q6IQ26	196
RAB41	RAB11FIP2	Q7L804	194
RAB41	GCC2	Q8IWJ2	190

IntAct

11 interactions, top by confidence:

A	B	Type	Score
RAB41	TCF4	psi-mi:“MI:0915”(physical association)	0.560
RAB41	REL	psi-mi:“MI:0915”(physical association)	0.560
TCF4	RAB41	psi-mi:“MI:0915”(physical association)	0.560
REL	RAB41	psi-mi:“MI:0915”(physical association)	0.560
RAB6B	SBF1	psi-mi:“MI:0914”(association)	0.530
RAB6B	RAB6A	psi-mi:“MI:0914”(association)	0.530
RAB41	PPP5C	psi-mi:“MI:0914”(association)	0.500
RAB41	PPP5C	psi-mi:“MI:0915”(physical association)	0.500

BioGRID (12): RAB41 (Two-hybrid), RAB41 (Two-hybrid), RAB41 (Two-hybrid), RAB41 (Affinity Capture-Western), RAB41 (Affinity Capture-MS), PPP5C (Affinity Capture-MS), FEM1B (Affinity Capture-MS), RAB41 (Two-hybrid), RAB41 (Affinity Capture-MS), FEM1B (Affinity Capture-MS), PPP5C (Affinity Capture-MS), RAB41 (Positive Genetic)

ESM2 similar proteins: A4D1S5, A6NH57, O45379, O59781, O88848, P25160, P25378, P34212, P38116, P40994, P51152, P51646, Q02804, Q0IIM2, Q13795, Q18510, Q2KJ96, Q32LJ2, Q3SXC5, Q54E92, Q54HK2, Q54I24, Q54JJ3, Q54V41, Q54V47, Q54Y14, Q54YV7, Q55AD9, Q5JT25, Q5M9P8, Q5R4G5, Q5R579, Q5RCQ6, Q60Z38, Q61DE0, Q63055, Q6P068, Q6P3A9, Q80ZU0, Q8BXL7

Diamond homologs: A4FV54, A6QR46, M0RC99, O18333, O18334, O80501, P05712, P11023, P16976, P17608, P18066, P20336, P20339, P20340, P22127, P22128, P24409, P25228, P29687, P31582, P31583, P34213, P35276, P35278, P35279, P35280, P35292, P36017, P36586, P36863, P49103, P49104, P51147, P51148, P53994, P55258, P61006, P61007, P61019, P61020

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	28
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1020 predictions. Top by Δscore:

Variant	Effect	Δscore
X:70282290:GAA:G	donor_gain	1.0000
X:70282329:G:GT	donor_gain	1.0000
X:70282331:A:T	donor_gain	1.0000
X:70282856:G:GG	donor_gain	1.0000
X:70283374:G:GG	donor_gain	1.0000
X:70283626:T:A	donor_loss	1.0000
X:70283938:T:A	acceptor_gain	1.0000
X:70283943:C:CA	acceptor_gain	1.0000
X:70283945:TCCA:T	acceptor_loss	1.0000
X:70283946:CCA:C	acceptor_loss	1.0000
X:70283948:A:AC	acceptor_loss	1.0000
X:70283948:A:AG	acceptor_gain	1.0000
X:70283949:G:GA	acceptor_gain	1.0000
X:70283949:GA:G	acceptor_gain	1.0000
X:70283949:GAC:G	acceptor_gain	1.0000
X:70283949:GACA:G	acceptor_gain	1.0000
X:70283949:GACAA:G	acceptor_gain	1.0000
X:70284040:AAAGG:A	donor_loss	1.0000
X:70284042:AGG:A	donor_loss	1.0000
X:70284044:G:GA	donor_loss	1.0000
X:70284045:T:A	donor_loss	1.0000
X:70284240:T:A	acceptor_gain	1.0000
X:70282286:A:T	donor_gain	0.9900
X:70282291:A:T	donor_gain	0.9900
X:70282297:A:AG	donor_gain	0.9900
X:70282298:G:GG	donor_gain	0.9900
X:70282339:GCGGT:G	donor_gain	0.9900
X:70282590:AGG:A	donor_loss	0.9900
X:70282591:GGTA:G	donor_loss	0.9900
X:70282592:G:C	donor_loss	0.9900

AlphaMissense

1466 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:70283287:A:C	D86A	0.994
X:70283307:T:C	F93L	0.993
X:70283309:T:A	F93L	0.993
X:70283309:T:G	F93L	0.993
X:70282542:C:T	T45I	0.992
X:70282540:G:C	K44N	0.991
X:70282540:G:T	K44N	0.991
X:70283286:G:C	D86H	0.990
X:70283287:A:T	D86V	0.990
X:70283288:C:A	D86E	0.990
X:70283288:C:G	D86E	0.990
X:70284014:A:C	S174R	0.990
X:70284016:T:A	S174R	0.990
X:70284016:T:G	S174R	0.990
X:70282538:A:C	K44Q	0.989
X:70284002:T:C	F170L	0.989
X:70284004:T:A	F170L	0.989
X:70284004:T:G	F170L	0.989
X:70282539:A:C	K44T	0.988
X:70282539:A:T	K44M	0.988
X:70282574:T:C	F56L	0.987
X:70282576:C:A	F56L	0.987
X:70282576:C:G	F56L	0.987
X:70283356:T:A	V109D	0.987
X:70282538:A:G	K44E	0.986
X:70283591:T:C	L141S	0.986
X:70283601:C:A	N144K	0.985
X:70283601:C:G	N144K	0.985
X:70283604:G:C	K145N	0.985
X:70283604:G:T	K145N	0.985

dbSNP variants (sampled 300 via entrez): RS1000410161 (X:70282104 C>T), RS1001006356 (X:70284456 C>T), RS1001267125 (X:70281398 G>A), RS1001340197 (X:70283554 G>A), RS1001613184 (X:70283032 C>G), RS1002459016 (X:70284944 C>A,T), RS1002619199 (X:70285394 C>T), RS1004121536 (X:70281292 T>C), RS1004165927 (X:70284968 T>C), RS1004519037 (X:70284491 C>G,T), RS1004854740 (X:70283723 C>A,T), RS1005524955 (X:70283168 C>G,T), RS1006118454 (X:70285470 G>A), RS1007920188 (X:70285125 AG>A), RS1009586777 (X:70282432 T>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
CGP 52608	increases reaction, affects binding	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation	1
Plant Extracts	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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