RGPD1

Summary

RGPD1 (RANBP2 like and GRIP domain containing 1, HGNC:32414) is a protein-coding gene on chromosome 2p11.2, encoding RANBP2-like and GRIP domain-containing protein 1 (P0DJD0).

Predicted to contribute to GTPase activator activity. Predicted to be involved in NLS-bearing protein import into nucleus. Predicted to be part of nuclear pore. Predicted to be active in cytoplasm.

Source: NCBI Gene 400966 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 59 total
• MANE Select transcript: NM_001382344

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32414
Approved symbol	RGPD1
Name	RANBP2 like and GRIP domain containing 1
Location	2p11.2
Locus type	gene with protein product
Status	Approved
Aliases	RGP1
Ensembl gene	ENSG00000187627
Ensembl biotype	protein_coding
OMIM	612704
Entrez	400966

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 nonsense_mediated_decay

ENST00000398193, ENST00000428128, ENST00000641339, ENST00000641458

RefSeq mRNA: 3 — MANE Select: NM_001382344 NM_001024457, NM_001382344, NM_001410915

CCDS: CCDS92799, CCDS92800

Canonical transcript exons

ENST00000641458 — 23 exons

Exon	Start	End
ENSE00002439417	86951296	86951360
ENSE00002444951	86976553	86976699
ENSE00002445323	86953498	86953650
ENSE00002445413	86963029	86963224
ENSE00002447396	86974073	86974254
ENSE00002448953	86976153	86976290
ENSE00002465737	86974681	86974804
ENSE00002481328	86974338	86974513
ENSE00002501260	86957706	86957936
ENSE00002515292	86969228	86969315
ENSE00002516856	86975728	86975886
ENSE00002522039	86952942	86953053
ENSE00002529542	86971747	86971956
ENSE00002535065	86958282	86958427
ENSE00002555416	87012513	87013976
ENSE00003468697	86984754	86984848
ENSE00003490846	86977848	86977931
ENSE00003511261	86997563	86997758
ENSE00003551374	86977580	86977759
ENSE00003568228	86994841	86994980
ENSE00003623273	86981083	86981200
ENSE00003672773	86985576	86987799
ENSE00003813190	86942118	86942308

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 95.09.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	95.09	gold quality
left testis	UBERON:0004533	95.07	gold quality
testis	UBERON:0000473	93.87	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.06	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.82	gold quality
placenta	UBERON:0001987	85.70	gold quality
pituitary gland	UBERON:0000007	80.81	gold quality
adenohypophysis	UBERON:0002196	80.25	gold quality
bone marrow cell	CL:0002092	78.93	gold quality
granulocyte	CL:0000094	78.59	gold quality
blood	UBERON:0000178	73.12	gold quality
endocervix	UBERON:0000458	72.72	gold quality
small intestine Peyer’s patch	UBERON:0003454	72.61	gold quality
lymph node	UBERON:0000029	71.86	gold quality
small intestine	UBERON:0002108	71.66	gold quality
bone marrow	UBERON:0002371	71.35	gold quality
tonsil	UBERON:0002372	70.65	gold quality
left uterine tube	UBERON:0001303	69.83	gold quality
mucosa of transverse colon	UBERON:0004991	69.80	gold quality
spleen	UBERON:0002106	69.58	gold quality
liver	UBERON:0002107	68.53	gold quality
duodenum	UBERON:0002114	68.34	gold quality
right coronary artery	UBERON:0001625	67.75	gold quality
stromal cell of endometrium	CL:0002255	67.72	gold quality
skeletal muscle tissue	UBERON:0001134	67.48	gold quality
right lobe of liver	UBERON:0001114	67.27	gold quality
body of pancreas	UBERON:0001150	67.03	gold quality
vermiform appendix	UBERON:0001154	66.13	gold quality
pancreas	UBERON:0001264	65.15	gold quality
muscle tissue	UBERON:0002385	64.73	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-86618	yes	105.61
E-ANND-3	yes	3.82
E-CURD-97	no	1411.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting RGPD1, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	ranbp3a	ENSDARG00000008727
drosophila_melanogaster	RanBP3	FBGN0039110

Paralogs (10): RGPD5 (ENSG00000015568), RANBP3 (ENSG00000031823), RANBP1 (ENSG00000099901), RGPD3 (ENSG00000153165), RANBP2 (ENSG00000153201), RANBP3L (ENSG00000164188), RGPD8 (ENSG00000169629), RGPD6 (ENSG00000183054), RGPD2 (ENSG00000185304), RGPD4 (ENSG00000196862)

Protein

Protein identifiers

RANBP2-like and GRIP domain-containing protein 1 — P0DJD0 (reviewed: P0DJD0)

Alternative names: Ran-binding protein 2-like 6

All UniProt accessions (4): A0A286YEQ5, A0A286YES2, F8VYC4, H7C1V8

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. One of the 8 copies of RANBP2 clustered close to the chromosome 2 centromere.

RefSeq proteins (3): NP_001019628, NP_001369273, NP_001397844 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000156	Ran_bind_dom	Domain
IPR000237	GRIP_dom	Domain
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR013105	TPR_2	Repeat
IPR019734	TPR_rpt	Repeat
IPR032023	GCC2_Rab_bind	Domain
IPR045255	RanBP1-like	Family

Pfam: PF00638, PF01465, PF07719, PF16704

UniProt features (19 total): compositionally biased region 5, region of interest 4, repeat 3, domain 3, sequence conflict 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DJD0-F1	66.21	0.31

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 158 (showing top): YAGI_AML_WITH_INV_16_TRANSLOCATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_REGULATION_OF_GTPASE_ACTIVITY, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOMF_GTPASE_BINDING, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_UP, GOBP_NUCLEAR_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, GOBP_REGULATION_OF_HYDROLASE_ACTIVITY, GOCC_TRANS_GOLGI_NETWORK, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION

GO Biological Process (2): NLS-bearing protein import into nucleus (GO:0006607), intracellular transport (GO:0046907)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): nuclear pore (GO:0005643), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	2
protein import into nucleus	1
transport	1
cellular localization	1
establishment of localization in cell	1
binding	1
nuclear envelope	1
nuclear protein-containing complex	1
cellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

13 interactions, top by confidence:

A	B	Type	Score
RAN	RGPD8	psi-mi:“MI:0914”(association)	0.640
RAN	NUP214	psi-mi:“MI:0914”(association)	0.350
RGPD1	RGPD3	psi-mi:“MI:0914”(association)	0.350
NPIPB6	GAPDHS	psi-mi:“MI:0914”(association)	0.350
RCC1	KPNA3	psi-mi:“MI:0914”(association)	0.350
SASS6	DVL2	psi-mi:“MI:2364”(proximity)	0.270
CEP63	CCDC66	psi-mi:“MI:2364”(proximity)	0.270
GLI2	CNOT1	psi-mi:“MI:2364”(proximity)	0.270
SOX9	BCL9	psi-mi:“MI:2364”(proximity)	0.270
STAT3	COPE	psi-mi:“MI:2364”(proximity)	0.270
RGPD1		psi-mi:“MI:0915”(physical association)	0.000
tap	RGPD1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (60): RGPD1 (Proximity Label-MS), RGPD1 (Proximity Label-MS), RGPD1 (Affinity Capture-MS), RGPD1 (Affinity Capture-MS), RGPD1 (Proximity Label-MS), RGPD1 (Proximity Label-MS), RGPD1 (Proximity Label-MS), RGPD1 (Proximity Label-MS), RGPD1 (Proximity Label-MS), RGPD1 (Proximity Label-MS), RGPD1 (Proximity Label-MS), RGPD1 (Proximity Label-MS), RGPD1 (Proximity Label-MS), RGPD1 (Proximity Label-MS), NUP85 (Affinity Capture-MS)

ESM2 similar proteins: A0A0B4K7J2, A1ZAK1, A6NKT7, F4J8D3, G5ED39, H2QII6, O01510, O14715, O48767, P0DJD0, P0DJD1, P12798, P33144, P40358, P42286, P49792, Q00416, Q0IEK6, Q18508, Q18892, Q20937, Q291E4, Q2U639, Q4WVM7, Q5B8K7, Q61CW2, Q61WP7, Q6C9G0, Q6CXL5, Q6FUS3, Q6FVG5, Q70PP2, Q751J3, Q754V0, Q759B7, Q759Y1, Q75B70, Q75CM2, Q7TSH2, Q7Z3J3

Diamond homologs: A0A0B4K7J2, A6NKT7, E9Q3G8, H2QII6, O14715, P0DJD0, P0DJD1, P34022, P40517, P41920, P43487, P92985, Q09717, Q3T0M7, Q54KD9, Q7Z3J3, Q8RWG8, Q99666, Q9C829, Q9LMK7, Q9USL4, D3ZZL9, P32499, P34562, P48820, P49792, Q8CHG3, Q8IWJ2, Q9ERU9, G0S8I1, Q09146, Q86VV4, A0A075B759, A0A075B767, A0A0B4J2A2, A0A0R0H9T5, A4FV72, D4AY02, F5H284, O00060

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4023 predictions. Top by Δscore:

Variant	Effect	Δscore
2:86922602:T:TA	acceptor_gain	1.0000
2:86922690:GAT:G	donor_gain	1.0000
2:86922693:G:GG	donor_gain	1.0000
2:86951294:A:AG	acceptor_gain	1.0000
2:86951295:G:GG	acceptor_gain	1.0000
2:86951295:GA:G	acceptor_gain	1.0000
2:86951295:GAA:G	acceptor_gain	1.0000
2:86951361:G:GG	donor_gain	1.0000
2:86953489:T:TA	acceptor_gain	1.0000
2:86953494:TTAGC:T	acceptor_loss	1.0000
2:86953495:TAG:T	acceptor_loss	1.0000
2:86953496:A:AG	acceptor_gain	1.0000
2:86953496:AGC:A	acceptor_gain	1.0000
2:86953496:AGCGT:A	acceptor_loss	1.0000
2:86953497:G:GA	acceptor_gain	1.0000
2:86953497:G:GC	acceptor_loss	1.0000
2:86953497:GC:G	acceptor_gain	1.0000
2:86953497:GCG:G	acceptor_gain	1.0000
2:86953625:G:GT	donor_gain	1.0000
2:86953646:TAAAG:T	donor_loss	1.0000
2:86953647:AAAG:A	donor_loss	1.0000
2:86953649:AGGT:A	donor_loss	1.0000
2:86953650:GG:G	donor_loss	1.0000
2:86953652:T:G	donor_loss	1.0000
2:86955724:A:G	donor_gain	1.0000
2:86955737:A:G	donor_gain	1.0000
2:86957700:A:AG	acceptor_gain	1.0000
2:86957701:A:G	acceptor_gain	1.0000
2:86957704:A:AG	acceptor_gain	1.0000
2:86957704:AG:A	acceptor_gain	1.0000

AlphaMissense

11582 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:86987160:T:A	W1413R	0.997
2:86987160:T:C	W1413R	0.997
2:86953000:G:C	G58R	0.996
2:86953001:G:A	G58D	0.996
2:86986897:T:C	L1325S	0.996
2:86986947:T:C	F1342L	0.995
2:86986949:T:A	F1342L	0.995
2:86986949:T:G	F1342L	0.995
2:86987265:G:C	A1448P	0.995
2:86987490:T:C	F1523L	0.994
2:86987492:T:A	F1523L	0.994
2:86987492:T:G	F1523L	0.994
2:86953499:G:C	R76P	0.993
2:86987056:G:C	R1378P	0.993
2:86987217:T:C	F1432L	0.993
2:86987218:T:C	F1432S	0.993
2:86987219:T:A	F1432L	0.993
2:86987219:T:G	F1432L	0.993
2:86952998:T:C	L57P	0.992
2:86953007:T:C	L60P	0.992
2:86986878:T:C	F1319L	0.992
2:86986880:T:A	F1319L	0.992
2:86986880:T:G	F1319L	0.992
2:86986900:C:A	P1326H	0.992
2:86952955:T:G	Y43D	0.991
2:86952977:A:G	D50G	0.991
2:86953048:T:G	Y74D	0.991
2:86986891:T:A	V1323D	0.991
2:86987026:T:C	I1368T	0.991
2:86987496:T:C	F1525L	0.991

dbSNP variants (sampled 300 via entrez): RS1000031346 (2:86929788 C>A,T), RS1000092262 (2:86940166 C>T), RS1000145615 (2:86918781 G>C), RS1000146035 (2:86940640 G>A), RS1000228908 (2:86944183 T>C), RS1000366425 (2:86919624 G>A), RS1000477391 (2:86924167 G>T), RS1000590871 (2:86931645 T>C), RS1000701238 (2:86924518 T>C), RS1001106318 (2:86979278 T>G), RS1001373370 (2:86989687 A>G), RS1001434962 (2:86993462 T>A), RS1001615899 (2:86941344 A>T), RS1001660575 (2:86931252 G>A), RS1001669814 (2:86941793 C>A,T)

Disease associations

OMIM: gene MIM:612704 | 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

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects expression, affects methylation	2
benzo(e)pyrene	decreases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
monomethylarsonous acid	decreases expression	1
pyrimidifen	decreases expression	1
bisphenol S	decreases methylation	1
Acetaminophen	decreases expression	1
Caffeine	decreases phosphorylation	1
Calcitriol	decreases expression	1
Lipopolysaccharides	increases expression, affects response to substance	1
Methapyrilene	decreases methylation	1
Valproic Acid	decreases methylation	1
Cyclosporine	increases methylation	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	increases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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