RAB6D

Summary

RAB6D (RAB6D, member RAS oncogene family, HGNC:30272) is a protein-coding gene on chromosome 2q21.1, encoding Ras-related protein Rab-6D (Q53S08). 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. Predicted to be involved in several processes, including Golgi vesicle transport; protein localization to Golgi membrane; and retrograde transport, endosome to Golgi. Located in Golgi apparatus; ciliary basal body; and nucleoplasm.

Source: NCBI Gene 150786 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001077637

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30272
Approved symbol	RAB6D
Name	RAB6D, member RAS oncogene family
Location	2q21.1
Locus type	gene with protein product
Status	Approved
Aliases	RAB6CL, WTH3DI
Ensembl gene	ENSG00000233087
Ensembl biotype	protein_coding
Entrez	150786

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000623617

RefSeq mRNA: 1 — MANE Select: NM_001077637 NM_001077637

CCDS: CCDS82514

Canonical transcript exons

ENST00000623617 — 1 exons

Exon	Start	End
ENSE00003758111	131360492	131364168

Expression profiles

Bgee: expression breadth broad, 62 present calls, max score 75.45.

Top tissues by expression

120 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	75.45	gold quality
superior frontal gyrus	UBERON:0002661	64.63	gold quality
quadriceps femoris	UBERON:0001377	64.14	gold quality
prefrontal cortex	UBERON:0000451	64.08	gold quality
cerebellar vermis	UBERON:0004720	63.05	gold quality
cortical plate	UBERON:0005343	61.25	gold quality
primary visual cortex	UBERON:0002436	61.08	gold quality
rectum	UBERON:0001052	60.15	gold quality
frontal cortex	UBERON:0001870	58.80	gold quality
Brodmann (1909) area 9	UBERON:0013540	58.10	gold quality
thymus	UBERON:0002370	57.37	silver quality
dorsolateral prefrontal cortex	UBERON:0009834	57.20	gold quality
cerebral cortex	UBERON:0000956	56.76	gold quality
islet of Langerhans	UBERON:0000006	56.66	gold quality
hypothalamus	UBERON:0001898	54.95	gold quality
prostate gland	UBERON:0002367	54.45	gold quality
anterior cingulate cortex	UBERON:0009835	53.43	gold quality
transverse colon	UBERON:0001157	53.37	gold quality
Ammon’s horn	UBERON:0001954	52.92	gold quality
ventricular zone	UBERON:0003053	52.20	silver quality
nucleus accumbens	UBERON:0001882	51.91	gold quality
right frontal lobe	UBERON:0002810	50.26	gold quality
smooth muscle tissue	UBERON:0001135	49.80	gold quality
temporal lobe	UBERON:0001871	49.65	gold quality
duodenum	UBERON:0002114	49.62	gold quality
amygdala	UBERON:0001876	49.45	gold quality
caudate nucleus	UBERON:0001873	49.34	gold quality
small intestine	UBERON:0002108	49.29	gold quality
gall bladder	UBERON:0002110	49.11	gold quality
stromal cell of endometrium	CL:0002255	48.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

115 targeting RAB6D, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-219A-5P	99.91	73.36	735
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-4782-3P	99.88	73.31	735
HSA-MIR-6766-3P	99.88	73.38	732
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-369-3P	99.85	70.52	2264

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-6D — Q53S08 (reviewed: Q53S08)

Alternative names: Rab6-like protein WTH3DI

All UniProt accessions (1): Q53S08

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.

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 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.

RefSeq proteins (1): NP_001071105* (*=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 (20 total): binding site 17, short sequence motif 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q53S08-F1	73.66	0.45

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): 39; 40; 42; 68; 71; 126; 127; 129; 157; 158; 23; 24 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 57 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, GOCC_MICROTUBULE_ORGANIZING_CENTER, 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, GOCC_CILIUM, GOCC_CILIARY_BASAL_BODY, GOMF_GTPASE_ACTIVITY, GOBP_GOLGI_VESICLE_TRANSPORT, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, 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 (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 (5): nucleoplasm (GO:0005654), Golgi apparatus (GO:0005794), cytosol (GO:0005829), endomembrane system (GO:0012505), ciliary basal body (GO:0036064)

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
catalytic activity	1
nuclear lumen	1
endomembrane system	1
intracellular membrane-bounded organelle	1
vacuole	1
plasma membrane	1
microtubule organizing center	1
cilium	1

Protein interactions and networks

STRING

330 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RAB6D	SCFD1	Q8WVM8	611
RAB6D	GDI2	P50395	609
RAB6D	USO1	O60763	597
RAB6D	RAB1A	P11476	402
RAB6D	RAB7A	P51149	400
RAB6D	RAB6A	P20340	364
RAB6D	DCTN6	O00399	325
RAB6D	A1CF	Q9NQ94	292
RAB6D	RINT1	Q6NUQ1	277
RAB6D	STX8	Q9UNK0	277
RAB6D	SYNGR1	O43759	269
RAB6D	RBM47	A0AV96	256
RAB6D	PIRT	P0C851	246
RAB6D	RTCB	Q9Y3I0	244
RAB6D	KIF18A	Q8NI77	222

IntAct

8 interactions, top by confidence:

A	B	Type	Score
SLC12A4	LGALS3	psi-mi:“MI:0914”(association)	0.530
RIN3		psi-mi:“MI:0914”(association)	0.350
RAB6C	CAPS	psi-mi:“MI:0914”(association)	0.350
SLC10A1	FLOT1	psi-mi:“MI:0914”(association)	0.350
SLC12A6	SCAMP1	psi-mi:“MI:0914”(association)	0.350
SLC2A3	NRP2	psi-mi:“MI:0914”(association)	0.350
CFTR	UBA6	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (9): WTH3DI (Affinity Capture-MS), WTH3DI (Affinity Capture-MS), WTH3DI (Affinity Capture-MS), WTH3DI (Affinity Capture-MS), WTH3DI (Cross-Linking-MS (XL-MS)), WTH3DI (Affinity Capture-MS), WTH3DI (Affinity Capture-MS), WTH3DI (Affinity Capture-MS), WTH3DI (Proximity Label-MS)

ESM2 similar proteins: A2YEQ6, O35963, O74536, O95661, O95755, P25378, P35283, P35284, P51156, P52198, P97950, Q00246, Q02723, Q06AU4, Q08AT1, Q08E00, Q09178, Q14088, Q20365, Q29RR0, Q3SXC5, Q3UHC2, Q504M8, Q53S08, Q5H913, Q5JT25, Q5R615, Q5U1Y1, Q5ZHV1, Q62120, Q62689, Q64008, Q69XM7, Q6IQ22, Q75R65, Q7SZ59, Q7TN89, Q7Z444, Q8C0V7, Q8CAM5

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1655 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:131363265:A:C	F152L	0.877
2:131363265:A:T	F152L	0.877
2:131363267:A:G	F152L	0.877
2:131363418:G:C	F101L	0.849
2:131363418:G:T	F101L	0.849
2:131363420:A:G	F101L	0.849
2:131363679:G:C	F14L	0.844
2:131363679:G:T	F14L	0.844
2:131363681:A:G	F14L	0.844
2:131363622:G:C	F33L	0.830
2:131363622:G:T	F33L	0.830
2:131363624:A:G	F33L	0.830
2:131363220:A:C	F167L	0.779
2:131363220:A:T	F167L	0.779
2:131363222:A:G	F167L	0.779
2:131363667:G:C	F18L	0.777
2:131363667:G:T	F18L	0.777
2:131363669:A:G	F18L	0.777
2:131363607:A:C	F38L	0.762
2:131363607:A:T	F38L	0.762
2:131363609:A:G	F38L	0.762
2:131363571:A:C	F50L	0.724
2:131363571:A:T	F50L	0.724
2:131363573:A:G	F50L	0.724
2:131363288:C:G	A145P	0.682
2:131363400:C:A	W107C	0.656
2:131363400:C:G	W107C	0.656
2:131363402:A:G	W107R	0.648
2:131363402:A:T	W107R	0.648
2:131363259:T:A	E154D	0.635

dbSNP variants (sampled 300 via entrez): RS1003672153 (2:131364083 G>A,C,T), RS1005653017 (2:131361270 C>T), RS1006169203 (2:131366058 TAAAG>T), RS1006614204 (2:131365883 T>TA), RS1007510626 (2:131360480 TCAAA>T), RS1007536705 (2:131360141 G>A), RS1007580529 (2:131361940 A>C,G), RS1008538129 (2:131361773 T>C), RS1010054361 (2:131362061 GT>G), RS1010437267 (2:131362420 A>G), RS1010720708 (2:131365176 C>T), RS1012041642 (2:131365862 A>G), RS1014675223 (2:131361233 TA>T), RS1014952551 (2:131365886 A>G), RS1015397618 (2:131365743 C>A,T)

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

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	increases phosphorylation	1
bisphenol A	decreases expression	1
sodium arsenite	affects cotreatment, increases expression	1
ferrous chloride	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Copper	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Tretinoin	increases expression, affects cotreatment	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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