RABAC1

Summary

RABAC1 (Rab acceptor 1, HGNC:9794) is a protein-coding gene on chromosome 19q13.2, encoding Prenylated Rab acceptor protein 1 (Q9UI14). General Rab protein regulator required for vesicle formation from the Golgi complex.

Enables identical protein binding activity. Located in membrane.

Source: NCBI Gene 10567 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 30 total
• MANE Select transcript: NM_006423

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9794
Approved symbol	RABAC1
Name	Rab acceptor 1
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	PRA1, PRAF1, YIP3
Ensembl gene	ENSG00000105404
Ensembl biotype	protein_coding
OMIM	604925
Entrez	10567

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 5 retained_intron

ENST00000222008, ENST00000595226, ENST00000596171, ENST00000598057, ENST00000599219, ENST00000600292, ENST00000601028, ENST00000601078, ENST00000601476, ENST00000601891, ENST00000903613, ENST00000918359, ENST00000918360, ENST00000918361, ENST00000918362

RefSeq mRNA: 1 — MANE Select: NM_006423 NM_006423

CCDS: CCDS12593

Canonical transcript exons

ENST00000222008 — 5 exons

Exon	Start	End
ENSE00000842521	41959237	41959321
ENSE00003490645	41958736	41958948
ENSE00003503818	41958286	41958383
ENSE00003604176	41957018	41957119
ENSE00003848497	41956683	41956934

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 102.4826 / max 774.0429, expressed in 1823 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
181104	101.1405	1822
208840	1.3250	919
181105	0.0171	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ascending aorta	UBERON:0001496	99.20	gold quality
thoracic aorta	UBERON:0001515	99.20	gold quality
pituitary gland	UBERON:0000007	99.17	gold quality
adenohypophysis	UBERON:0002196	99.16	gold quality
descending thoracic aorta	UBERON:0002345	99.14	gold quality
left coronary artery	UBERON:0001626	99.08	gold quality
stromal cell of endometrium	CL:0002255	99.07	gold quality
endocervix	UBERON:0000458	99.03	gold quality
body of uterus	UBERON:0009853	99.01	gold quality
hypothalamus	UBERON:0001898	98.99	gold quality
popliteal artery	UBERON:0002250	98.94	gold quality
tibial artery	UBERON:0007610	98.94	gold quality
right coronary artery	UBERON:0001625	98.93	gold quality
fundus of stomach	UBERON:0001160	98.88	gold quality
myometrium	UBERON:0001296	98.88	gold quality
mucosa of transverse colon	UBERON:0004991	98.87	gold quality
left uterine tube	UBERON:0001303	98.86	gold quality
lower esophagus muscularis layer	UBERON:0035833	98.86	gold quality
substantia nigra	UBERON:0002038	98.85	gold quality
lower esophagus	UBERON:0013473	98.85	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	98.85	gold quality
mucosa of stomach	UBERON:0001199	98.83	gold quality
right ovary	UBERON:0002118	98.82	gold quality
body of stomach	UBERON:0001161	98.81	gold quality
right lobe of thyroid gland	UBERON:0001119	98.80	gold quality
putamen	UBERON:0001874	98.80	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.80	gold quality
muscle layer of sigmoid colon	UBERON:0035805	98.78	gold quality
left testis	UBERON:0004533	98.77	gold quality
right testis	UBERON:0004534	98.76	gold quality

Single-cell (SCXA)

Detected in 15 experiment(s), a significant marker in 12.

Experiment	Marker?	Max mean expression
E-CURD-88	yes	85.19
E-MTAB-9467	yes	64.40
E-MTAB-6701	yes	51.80
E-HCAD-1	yes	51.75
E-HCAD-4	yes	44.16
E-CURD-46	yes	43.49
E-CURD-122	yes	42.35
E-ANND-3	yes	28.68
E-HCAD-9	yes	17.27
E-CURD-112	yes	14.59
E-MTAB-10553	yes	9.33
E-MTAB-10042	yes	8.90
E-GEOD-36552	no	175.24
E-HCAD-8	no	29.93
E-CURD-114	no	18.09

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting RABAC1, 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-1286	99.09	66.23	1046
HSA-MIR-4745-3P	83.50	60.58	126
HSA-MIR-5587-3P	82.90	60.79	138

Literature-anchored findings (GeneRIF, showing 7)

• findings show Yip3 acts catalytically to dissociate complexes of endosomal Rabs bound to GDI and to deliver them onto membranes; propose that the conserved Yip proteins serve as GDI-displacement factors for the targeting of Rab GTPases in eukaryotic cells (PMID:14574414)
• Coexpression of a PRA1 export mutant or knockdown of PRA1 led to redistribution of LMP1 and its associated signaling molecules to the endoplasmic reticulum and subsequent impairment of LMP1-induced NF-kappaB activation. (PMID:16917502)
• in vivo modulation of PRA1 may be involved in TCF/beta-catenin signaling, as well as cellular proliferation and tumorigenesis (PMID:16930546)
• These findings delineated novel roles of PRA1 in lipid transport and cell migration. (PMID:20592422)
• Prenylated Rab acceptor protein 1 (PRA1) was identified as an interacting partner of SNCA. (PMID:21798244)
• Results suggest that NDRG2 and prenylated Rab acceptor-1 (PRA1) might act synergistically to prevent signaling of T-cell facto/beta-catenin. (PMID:23068607)
• RABAC1 caused caspase-3 activation and decreased cell proliferation, clonogenic cell survival, and cell migration and invasion. (PMID:31003775)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rabac1	ENSDARG00000004171
mus_musculus	Rabac1	ENSMUSG00000003380
rattus_norvegicus	Rabac1	ENSRNOG00000020233
drosophila_melanogaster	CG1418	FBGN0033468

Protein

Protein identifiers

Prenylated Rab acceptor protein 1 — Q9UI14 (reviewed: Q9UI14)

Alternative names: PRA1 family protein 1

All UniProt accessions (5): Q9UI14, M0QXH1, M0QXU8, M0R1H9, M0R3D4

UniProt curated annotations — full annotation on UniProt →

Function. General Rab protein regulator required for vesicle formation from the Golgi complex. May control vesicle docking and fusion by mediating the action of Rab GTPases to the SNARE complexes. In addition it inhibits the removal of Rab GTPases from the membrane by GDI.

Subunit / interactions. Homodimer. Interacts with VAMP2 (synaptobrevin-2), GDI1, and PCLO. Interacts specifically with prenylated Rab proteins; strongly with RAB4B, RAB5A and RAB5C, and weakly with RAB4A, RAB6, RAB7A, RAB17 and RAB22. Interacts with NDRG1.

Subcellular location. Cell membrane. Cytoplasm. Golgi apparatus. Cytoplasmic vesicle. Secretory vesicle. Synaptic vesicle.

Tissue specificity. Ubiquitous. Strongest expression found in placenta, pituitary gland, kidney, lung and stomach.

Similarity. Belongs to the PRA1 family.

RefSeq proteins (1): NP_006414* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004895	Prenylated_rab_accept_PRA1	Family

Pfam: PF03208

UniProt features (15 total): region of interest 4, transmembrane region 4, topological domain 3, sequence conflict 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UI14-F1	83.54	0.50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 178 (showing top): MYAATNNNNNNNGGC_UNKNOWN, ENK_UV_RESPONSE_KERATINOCYTE_UP, GCANCTGNY_MYOD_Q6, KAAB_HEART_ATRIUM_VS_VENTRICLE_UP, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, GOMF_GTPASE_BINDING, CAGCTG_AP4_Q5, AACWWCAANK_UNKNOWN, GALE_APL_WITH_FLT3_MUTATED_DN, KOYAMA_SEMA3B_TARGETS_UP, MORF_PML, MORF_IKBKG, ZAMORA_NOS2_TARGETS_DN, GOCC_EXOCYTIC_VESICLE, GOCC_SECRETORY_VESICLE

GO Biological Process (0):

GO Molecular Function (4): identical protein binding (GO:0042802), GTPase binding (GO:0051020), proline-rich region binding (GO:0070064), protein binding (GO:0005515)

GO Cellular Component (9): Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), synaptic vesicle (GO:0008021), membrane (GO:0016020), glutamatergic synapse (GO:0098978), cytoplasm (GO:0005737), cytoplasmic vesicle (GO:0031410), synapse (GO:0045202), presynapse (GO:0098793)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
protein binding	2
cytoplasm	2
synapse	2
enzyme binding	1
binding	1
endomembrane system	1
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1
exocytic vesicle	1
presynapse	1
intracellular anatomical structure	1
intracellular vesicle	1
cell junction	1

Protein interactions and networks

STRING

1326 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RABAC1	PCLO	Q9Y6V0	870
RABAC1	PLG	P00747	856
RABAC1	RAPGEF4	Q8WZA2	783
RABAC1	ARL6IP5	O75915	772
RABAC1	RIMS2	Q9UQ26	761
RABAC1	VAMP2	P19065	748
RABAC1	PRAF2	O60831	667
RABAC1	RAB3A	P20336	624
RABAC1	SYT1	P21579	595
RABAC1	YIF1A	O95070	548
RABAC1	RBBP8	Q99708	548
RABAC1	C4A	P01028	545
RABAC1	C4A	P01028	527
RABAC1	RAB6A	P20340	515
RABAC1	RAB4B	P22750	514

IntAct

346 interactions, top by confidence:

A	B	Type	Score
RABAC1	COQ8A	psi-mi:“MI:0915”(physical association)	0.850
COQ8A	RABAC1	psi-mi:“MI:0915”(physical association)	0.850
RABAC1	NTAQ1	psi-mi:“MI:0915”(physical association)	0.840
NTAQ1	RABAC1	psi-mi:“MI:0915”(physical association)	0.840
RABAC1	SYT16	psi-mi:“MI:0915”(physical association)	0.830
RABAC1	RABAC1	psi-mi:“MI:0915”(physical association)	0.830
SYT16	RABAC1	psi-mi:“MI:0915”(physical association)	0.830
TRIM32	RABAC1	psi-mi:“MI:0915”(physical association)	0.810
RABAC1	TRIM32	psi-mi:“MI:0915”(physical association)	0.810

BioGRID (200): RABAC1 (Two-hybrid), RABAC1 (Two-hybrid), DUSP12 (Two-hybrid), TRIM32 (Two-hybrid), WIPI2 (Two-hybrid), SNX10 (Two-hybrid), SNX15 (Two-hybrid), SNX11 (Two-hybrid), SPG21 (Two-hybrid), WDYHV1 (Two-hybrid), ADCK3 (Two-hybrid), RIC8A (Two-hybrid), NDRG4 (Two-hybrid), ZFYVE21 (Two-hybrid), SYT16 (Two-hybrid)

ESM2 similar proteins: A4FUB8, E9QBI7, O35394, O95070, O97681, P15920, P58872, P58873, Q0DWA9, Q0P5E4, Q12270, Q12893, Q13488, Q1RMH4, Q28C60, Q3UVK0, Q4V8F3, Q52NJ0, Q5RBS4, Q5XIT3, Q5Z413, Q6BSA9, Q6C741, Q6CDV6, Q6CR06, Q6DCK1, Q6FSG0, Q6P6G5, Q6UPR8, Q755H8, Q7Z2K6, Q874X5, Q8BHC7, Q8BXJ9, Q8RXQ2, Q8TEB9, Q8VC82, Q8VZ96, Q91VU1, Q91XB7

Diamond homologs: O35394, Q1RMH4, Q52NJ0, Q54XK1, Q8HY39, Q9LYN0, Q9UI14, Q9UUN5, Q9Z0S9, O80915, P93829, Q9C889, Q9FH16, Q9FLB6, Q9FRR1, Q9FZ63, Q9LIC6, Q9LIC7, Q9LYQ4, Q9M012, Q9SIY7, Q9ZWD1, P53633

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 71 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.

GO biological processes:

GO term	Partners	Fold	FDR
intracellular protein transport	7	8.2×	5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

674 predictions. Top by Δscore:

Variant	Effect	Δscore
19:41956932:CTC:C	acceptor_gain	1.0000
19:41956935:C:CC	acceptor_gain	1.0000
19:41956935:CTG:C	acceptor_loss	1.0000
19:41957016:AC:A	donor_gain	1.0000
19:41957017:CC:C	donor_gain	1.0000
19:41958731:CTCA:C	donor_loss	1.0000
19:41958733:CA:C	donor_loss	1.0000
19:41958734:A:AC	donor_gain	1.0000
19:41958734:AC:A	donor_loss	1.0000
19:41958735:C:CC	donor_gain	1.0000
19:41958735:CA:C	donor_gain	1.0000
19:41958735:CACA:C	donor_gain	1.0000
19:41958773:A:AC	donor_gain	1.0000
19:41958774:G:C	donor_gain	1.0000
19:41958791:C:CA	donor_gain	1.0000
19:41959128:T:TA	donor_gain	1.0000
19:41959196:C:CA	donor_gain	1.0000
19:41956930:GGCTC:G	acceptor_gain	0.9900
19:41956933:TC:T	acceptor_gain	0.9900
19:41956934:CC:C	acceptor_gain	0.9900
19:41957009:TGTAC:T	donor_loss	0.9900
19:41957010:GTACT:G	donor_loss	0.9900
19:41957011:TACT:T	donor_loss	0.9900
19:41957012:ACTC:A	donor_loss	0.9900
19:41957013:CTC:C	donor_loss	0.9900
19:41957014:T:TC	donor_loss	0.9900
19:41957015:C:CC	donor_loss	0.9900
19:41957016:ACCC:A	donor_loss	0.9900
19:41957017:C:A	donor_loss	0.9900
19:41957017:CCCAG:C	donor_gain	0.9900

AlphaMissense

1173 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:41958774:G:C	N77K	0.999
19:41958774:G:T	N77K	0.999
19:41957018:C:G	G157R	0.998
19:41957018:C:T	G157R	0.998
19:41957032:A:T	V152D	0.998
19:41957083:G:T	A135D	0.998
19:41958339:C:T	G105D	0.998
19:41956934:C:T	G157E	0.997
19:41958872:A:G	W45R	0.997
19:41958872:A:T	W45R	0.997
19:41956901:G:T	A168D	0.996
19:41956904:G:T	A167D	0.996
19:41956913:C:T	G164D	0.996
19:41956914:C:G	G164R	0.996
19:41957080:C:T	G136E	0.996
19:41958348:A:T	V102D	0.996
19:41958743:A:C	Y88D	0.996
19:41957027:A:G	W154R	0.995
19:41957027:A:T	W154R	0.995
19:41957050:G:T	A146D	0.995
19:41957065:G:C	P141R	0.995
19:41957081:C:G	G136R	0.995
19:41957081:C:T	G136R	0.995
19:41958340:C:G	G105R	0.995
19:41958366:A:G	L96S	0.995
19:41958740:A:G	C89R	0.995
19:41958755:C:G	G84R	0.995
19:41958862:A:G	F48S	0.995
19:41956908:G:C	H166D	0.994
19:41956931:G:T	A158D	0.994

dbSNP variants (sampled 300 via entrez): RS1000236989 (19:41957790 T>G), RS1002177196 (19:41959159 C>G,T), RS1003010239 (19:41956247 C>G), RS1003227137 (19:41960928 C>T), RS1003584262 (19:41960546 T>A), RS1003952040 (19:41960527 A>G), RS1007504626 (19:41957254 C>G), RS1007824070 (19:41957064 G>A), RS1008182844 (19:41959916 G>A), RS1009529160 (19:41959589 G>C), RS1010544753 (19:41961152 A>G), RS1011204054 (19:41960943 G>A,T), RS1011531921 (19:41959341 A>C,G), RS1013607247 (19:41958714 G>A,T), RS1013659315 (19:41959115 C>T)

Disease associations

OMIM: gene MIM:604925 | 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):

Study	Trait	p-value
GCST010703_14	Brain morphology (MOSTest)	1.000000e-09
GCST90013421_21	Left-handedness	6.000000e-15

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0009902	handedness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	3
Tetrachlorodibenzodioxin	increases expression	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
methylselenic acid	decreases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	increases abundance, increases expression	1
perfluorooctanoic acid	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	increases reaction, affects binding	1
corosolic acid	increases expression	1
jinfukang	increases expression	1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Vorinostat	decreases expression	1
Air Pollutants	increases abundance, decreases expression	1
Arsenic	increases abundance, increases expression	1
Atrazine	increases expression	1
Doxorubicin	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Quercetin	increases expression	1
Selenium	increases expression	1
Tunicamycin	increases expression	1
Valproic Acid	increases expression	1
Vitamin E	increases expression	1
Asbestos, Crocidolite	increases expression	1
Thapsigargin	increases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	increases abundance, decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2D7	Abcam HeLa RABAC1 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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