RGPD2

Summary

RGPD2 (RANBP2 like and GRIP domain containing 2, HGNC:32415) is a protein-coding gene on chromosome 2p11.2, encoding RANBP2-like and GRIP domain-containing protein 2 (P0DJD1).

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 729857 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 69 total
• MANE Select transcript: NM_001078170

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32415
Approved symbol	RGPD2
Name	RANBP2 like and GRIP domain containing 2
Location	2p11.2
Locus type	gene with protein product
Status	Approved
Aliases	RGP2, RANBP2L2
Ensembl gene	ENSG00000185304
Ensembl biotype	protein_coding
OMIM	612705
Entrez	729857

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000398146, ENST00000494592, ENST00000971290

RefSeq mRNA: 2 — MANE Select: NM_001078170 NM_001078170, NM_001393613

CCDS: CCDS42710

Canonical transcript exons

ENST00000398146 — 23 exons

Exon	Start	End
ENSE00001473300	87755960	87757426
ENSE00002438786	87788722	87788839
ENSE00002451770	87785075	87785169
ENSE00002467654	87772169	87772364
ENSE00002508834	87791990	87792073
ENSE00002530390	87774944	87775083
ENSE00002534099	87782124	87784347
ENSE00003458440	87794035	87794193
ENSE00003464122	87795117	87795240
ENSE00003470454	87800605	87800692
ENSE00003477791	87818559	87818623
ENSE00003529441	87793222	87793368
ENSE00003544373	87806696	87806891
ENSE00003547057	87816866	87816977
ENSE00003566563	87797965	87798174
ENSE00003582941	87792162	87792341
ENSE00003586343	87816269	87816421
ENSE00003590108	87811485	87811630
ENSE00003612732	87793631	87793768
ENSE00003625204	87795667	87795848
ENSE00003630053	87795408	87795583
ENSE00003686546	87811976	87812206
ENSE00003809404	87825658	87825796

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 90.04.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	90.04	gold quality
right testis	UBERON:0004534	90.03	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.98	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.77	gold quality
testis	UBERON:0000473	89.38	gold quality
endocervix	UBERON:0000458	80.58	gold quality
right lobe of liver	UBERON:0001114	80.04	gold quality
granulocyte	CL:0000094	79.37	gold quality
placenta	UBERON:0001987	78.46	gold quality
bone marrow cell	CL:0002092	76.93	gold quality
adenohypophysis	UBERON:0002196	76.18	gold quality
bone marrow	UBERON:0002371	75.69	gold quality
pituitary gland	UBERON:0000007	75.63	gold quality
liver	UBERON:0002107	75.18	gold quality
blood	UBERON:0000178	74.86	gold quality
body of pancreas	UBERON:0001150	74.23	gold quality
left uterine tube	UBERON:0001303	73.45	gold quality
descending thoracic aorta	UBERON:0002345	71.95	gold quality
mucosa of stomach	UBERON:0001199	71.92	gold quality
pancreas	UBERON:0001264	71.90	gold quality
ventricular zone	UBERON:0003053	71.67	gold quality
uterine cervix	UBERON:0000002	71.51	gold quality
spleen	UBERON:0002106	71.41	gold quality
small intestine Peyer’s patch	UBERON:0003454	71.33	gold quality
lymph node	UBERON:0000029	71.08	gold quality
right coronary artery	UBERON:0001625	71.08	gold quality
mucosa of transverse colon	UBERON:0004991	71.01	gold quality
ectocervix	UBERON:0012249	70.49	gold quality
cortical plate	UBERON:0005343	70.22	gold quality
endometrium	UBERON:0001295	70.16	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.88
E-CURD-89	no	393.67
E-CURD-95	no	256.53

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting RGPD2, 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-96-5P	99.95	72.80	2140
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-1324	99.46	66.57	1302
HSA-MIR-593-5P	99.34	69.50	965
HSA-MIR-6715B-3P	98.80	68.07	1204
HSA-MIR-4742-3P	98.73	69.82	1803
HSA-MIR-4752	98.71	68.04	833
HSA-MIR-6792-5P	98.39	68.16	1330
HSA-MIR-3166	98.24	66.63	1223

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), RGPD1 (ENSG00000187627), RGPD4 (ENSG00000196862)

Protein

Protein identifiers

RANBP2-like and GRIP domain-containing protein 2 — P0DJD1 (reviewed: P0DJD1)

Alternative names: Ran-binding protein 2-like 2

All UniProt accessions (1): P0DJD1

UniProt curated annotations — full annotation on UniProt →

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

RefSeq proteins (2): NP_001071638, NP_001380542 (=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 (17 total): compositionally biased region 5, region of interest 4, repeat 3, domain 3, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DJD1-F1	66.27	0.25

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): 21

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 32 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_NUCLEAR_TRANSPORT, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, chr2p11, GOBP_NLS_BEARING_PROTEIN_IMPORT_INTO_NUCLEUS, GOBP_NUCLEAR_EXPORT, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_PROTEIN_LOCALIZATION_TO_NUCLEUS, GOCC_NUCLEAR_ENVELOPE, GOCC_NUCLEAR_PORE, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_SUMO_TRANSFERASE_ACTIVITY, GOMF_AMINOACYLTRANSFERASE_ACTIVITY, GOCC_ORGANELLE_ENVELOPE

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

GO Molecular Function (2): GTPase activator activity (GO:0005096), 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
GTPase activity	1
enzyme activator activity	1
GTPase regulator activity	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

20 interactions, top by confidence:

A	B	Type	Score
BCL2	BCL2L11	psi-mi:“MI:0914”(association)	0.930
EXOC3	EXOC5	psi-mi:“MI:0914”(association)	0.790
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
NEMP1	RGPD8	psi-mi:“MI:0914”(association)	0.640
RAN	NEMP2	psi-mi:“MI:0914”(association)	0.530
B2M	KPNA3	psi-mi:“MI:0914”(association)	0.530
TACR1	GPR89A	psi-mi:“MI:0914”(association)	0.350
CLRN2	FAM234B	psi-mi:“MI:0914”(association)	0.350
CHRNB2	TMEM131L	psi-mi:“MI:0914”(association)	0.350
DGCR2	CCDC85C	psi-mi:“MI:0914”(association)	0.350
U2AF1	RGPD2	psi-mi:“MI:0914”(association)	0.350
NTNG1	UBA6	psi-mi:“MI:0914”(association)	0.350
UBE2I	RGPD2	psi-mi:“MI:0914”(association)	0.350

BioGRID (34): RGPD2 (Co-fractionation), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), RGPD2 (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, A0A075B759, A0A075B767, A0A0B4J2A2, A0A0R0H9T5, A4FV72, D4AY02, F5H284, O00060, O49886, O93826, P0C1H7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	64
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3641 predictions. Top by Δscore:

Variant	Effect	Δscore
2:87772156:T:A	donor_gain	1.0000
2:87772165:CCA:C	donor_loss	1.0000
2:87772166:CAC:C	donor_loss	1.0000
2:87772167:ACCT:A	donor_loss	1.0000
2:87772168:CCTTG:C	donor_loss	1.0000
2:87772361:GAAG:G	acceptor_gain	1.0000
2:87772365:C:CC	acceptor_gain	1.0000
2:87772368:G:GC	acceptor_gain	1.0000
2:87772371:T:C	acceptor_gain	1.0000
2:87772371:T:TC	acceptor_gain	1.0000
2:87784346:CC:C	acceptor_gain	1.0000
2:87784347:CC:C	acceptor_gain	1.0000
2:87785064:T:TA	donor_gain	1.0000
2:87785170:C:CC	acceptor_gain	1.0000
2:87788717:CTCA:C	donor_loss	1.0000
2:87788718:TCACC:T	donor_loss	1.0000
2:87788719:CACCT:C	donor_loss	1.0000
2:87788721:CCTG:C	donor_loss	1.0000
2:87788835:AGTTT:A	acceptor_gain	1.0000
2:87788836:GTTT:G	acceptor_gain	1.0000
2:87788837:TTT:T	acceptor_gain	1.0000
2:87788838:TT:T	acceptor_gain	1.0000
2:87788839:TC:T	acceptor_loss	1.0000
2:87788840:C:CA	acceptor_loss	1.0000
2:87788840:C:CC	acceptor_gain	1.0000
2:87788843:T:C	acceptor_gain	1.0000
2:87788843:T:TC	acceptor_gain	1.0000
2:87791985:CTTA:C	donor_loss	1.0000
2:87791986:TTACC:T	donor_loss	1.0000
2:87791988:A:AC	donor_gain	1.0000

AlphaMissense

11584 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:87782763:A:G	W1421R	0.995
2:87782763:A:T	W1421R	0.995
2:87782705:A:G	F1440S	0.993
2:87782704:A:C	F1440L	0.992
2:87782704:A:T	F1440L	0.992
2:87782706:A:G	F1440L	0.992
2:87816918:C:T	G66D	0.992
2:87782431:A:C	F1531L	0.991
2:87782431:A:T	F1531L	0.991
2:87782433:A:G	F1531L	0.991
2:87782658:C:G	A1456P	0.991
2:87782974:A:C	F1350L	0.991
2:87782974:A:T	F1350L	0.991
2:87782976:A:G	F1350L	0.991
2:87782711:A:T	V1438D	0.990
2:87782928:A:G	W1366R	0.989
2:87782928:A:T	W1366R	0.989
2:87816919:C:G	G66R	0.989
2:87782761:C:A	W1421C	0.988
2:87782761:C:G	W1421C	0.988
2:87793271:A:G	L717P	0.988
2:87800612:G:C	S352R	0.988
2:87800612:G:T	S352R	0.988
2:87800614:T:G	S352R	0.988
2:87782897:A:G	I1376T	0.987
2:87782715:C:G	A1437P	0.986
2:87782746:A:C	F1426L	0.986
2:87782746:A:T	F1426L	0.986
2:87782748:A:G	F1426L	0.986
2:87782678:A:G	F1449S	0.985

dbSNP variants (sampled 300 via entrez): RS1000062645 (2:87923865 G>T), RS1000116964 (2:87841319 G>C), RS1000150387 (2:87858627 A>G,T), RS1000197961 (2:87853885 C>A), RS1000215405 (2:87936351 G>T), RS1000256502 (2:87979255 A>G), RS1000271674 (2:87853523 T>C), RS1000340707 (2:87948567 G>C), RS1000407093 (2:87914656 T>G), RS1000435622 (2:87948201 C>G), RS1000491761 (2:87961395 C>A,G), RS1000535719 (2:87850341 C>G,T), RS1000572495 (2:87841141 C>T), RS1000579481 (2:87934496 G>A,C,T), RS1000609287 (2:87849965 T>G)

Disease associations

OMIM: gene MIM:612705 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001471_2	Alcohol and nicotine co-dependence	3.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
Arsenic	affects methylation	1
Diethylhexyl Phthalate	decreases expression	1
Lipopolysaccharides	increases expression, affects response to substance, affects cotreatment	1
Tobacco Smoke Pollution	increases expression	1

Clinical trials (associated diseases)

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