RGPD4

Summary

RGPD4 (RANBP2 like and GRIP domain containing 4, HGNC:32417) is a protein-coding gene on chromosome 2q12.3, encoding RanBP2-like and GRIP domain-containing protein 4 (Q7Z3J3). It is a selective cancer dependency (DepMap: 16.4% of cell lines).

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 285190 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 373 total
• Cancer dependency (DepMap): dependent in 16.4% of screened cell lines
• MANE Select transcript: NM_182588

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32417
Approved symbol	RGPD4
Name	RANBP2 like and GRIP domain containing 4
Location	2q12.3
Locus type	gene with protein product
Status	Approved
Aliases	RGP4, DKFZp686P0288
Ensembl gene	ENSG00000196862
Ensembl biotype	protein_coding
OMIM	612707
Entrez	285190

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000408999

RefSeq mRNA: 1 — MANE Select: NM_182588 NM_182588

CCDS: CCDS46381

Canonical transcript exons

ENST00000408999 — 23 exons

Exon	Start	End
ENSE00001872929	107826892	107827085
ENSE00001910458	107890721	107892544
ENSE00002445986	107861194	107861331
ENSE00002452314	107862949	107863032
ENSE00002455397	107869883	107869977
ENSE00002457670	107859722	107859845
ENSE00002464767	107843009	107843239
ENSE00002471423	107838812	107838964
ENSE00002478426	107843585	107843730
ENSE00002483308	107861594	107861740
ENSE00002483655	107882672	107882873
ENSE00002483815	107854556	107854643
ENSE00002486568	107866190	107866325
ENSE00002495853	107836602	107836669
ENSE00002500115	107862682	107862861
ENSE00002505121	107838257	107838368
ENSE00002514284	107879968	107880107
ENSE00002520911	107859114	107859295
ENSE00002524501	107870705	107872928
ENSE00002525608	107859379	107859554
ENSE00002526803	107860766	107860927
ENSE00002527577	107856760	107856969
ENSE00002530598	107848341	107848536

Expression profiles

Bgee: expression breadth ubiquitous, 120 present calls, max score 76.70.

Top tissues by expression

131 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	76.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.24	gold quality
testis	UBERON:0000473	62.13	gold quality
left testis	UBERON:0004533	61.38	gold quality
right testis	UBERON:0004534	61.06	gold quality
mucosa of transverse colon	UBERON:0004991	59.85	gold quality
ventricular zone	UBERON:0003053	57.98	gold quality
primary visual cortex	UBERON:0002436	56.96	gold quality
hindlimb stylopod muscle	UBERON:0004252	56.24	gold quality
islet of Langerhans	UBERON:0000006	54.64	gold quality
superior frontal gyrus	UBERON:0002661	54.17	gold quality
ganglionic eminence	UBERON:0004023	53.04	silver quality
granulocyte	CL:0000094	52.29	gold quality
endometrium	UBERON:0001295	51.05	gold quality
urinary bladder	UBERON:0001255	50.86	gold quality
pancreas	UBERON:0001264	50.55	gold quality
right lobe of liver	UBERON:0001114	50.43	gold quality
tibial artery	UBERON:0007610	50.24	gold quality
popliteal artery	UBERON:0002250	50.23	gold quality
colonic epithelium	UBERON:0000397	50.09	gold quality
putamen	UBERON:0001874	50.08	gold quality
muscle of leg	UBERON:0001383	49.95	gold quality
gastrocnemius	UBERON:0001388	49.90	gold quality
anterior cingulate cortex	UBERON:0009835	49.78	gold quality
Brodmann (1909) area 9	UBERON:0013540	49.27	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	49.23	gold quality
liver	UBERON:0002107	49.18	silver quality
lower esophagus mucosa	UBERON:0035834	49.11	gold quality
left adrenal gland cortex	UBERON:0035825	49.09	gold quality
body of pancreas	UBERON:0001150	48.98	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

113 targeting RGPD4, 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-513A-5P	100.00	69.77	2465
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-4267	99.96	66.53	2368

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 16.4% of screened cell lines.

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), RGPD1 (ENSG00000187627)

Protein

Protein identifiers

RanBP2-like and GRIP domain-containing protein 4 — Q7Z3J3 (reviewed: Q7Z3J3)

All UniProt accessions (1): Q7Z3J3

UniProt curated annotations — full annotation on UniProt →

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q7Z3J3-1	1	yes
Q7Z3J3-2	2

RefSeq proteins (1): NP_872394* (*=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
IPR019734	TPR_rpt	Repeat
IPR032023	GCC2_Rab_bind	Domain
IPR045255	RanBP1-like	Family

Pfam: PF00638, PF01465, PF13181, PF16704

UniProt features (19 total): compositionally biased region 6, region of interest 4, domain 3, repeat 2, splice variant 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z3J3-F1	67.37	0.27

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: 55 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, chr2q12, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_NUCLEAR_TRANSPORT, MARZEC_IL2_SIGNALING_DN, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_NLS_BEARING_PROTEIN_IMPORT_INTO_NUCLEUS, GOBP_NUCLEAR_EXPORT, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GOBP_PROTEIN_LOCALIZATION_TO_NUCLEUS, GOCC_NUCLEAR_ENVELOPE, GOCC_NUCLEAR_PORE, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_SUMO_TRANSFERASE_ACTIVITY, GOMF_AMINOACYLTRANSFERASE_ACTIVITY

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

1636 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RGPD4	GRIP1	Q9Y3R0	706
RGPD4	USP17L13	C9JLJ4	570
RGPD4	SUMO1	P55856	471
RGPD4	C16orf90	A8MZG2	440
RGPD4	WFDC11	Q8NEX6	436
RGPD4	IQCF3	P0C7M6	413
RGPD4	SPANXN5	Q5MJ07	405
RGPD4	AADACL2	Q6P093	395
RGPD4	TXNDC8	Q6A555	369
RGPD4	DEFB112	Q30KQ8	368
RGPD4	GCC2	Q8IWJ2	366
RGPD4	POTEH	Q6S545	355
RGPD4	SH3TC1	Q8TE82	349
RGPD4	CIB4	A0PJX0	338
RGPD4	SIRAL2	Q9NWS6	326

IntAct

9 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
RAN	RGPD8	psi-mi:“MI:0914”(association)	0.640
PLK1	ERCC6L	psi-mi:“MI:0914”(association)	0.350
UVRAG	DFFA	psi-mi:“MI:0914”(association)	0.350
KPNA4	POM121C	psi-mi:“MI:0914”(association)	0.350
NUMA1	SHANK3	psi-mi:“MI:0914”(association)	0.350
RAN	NUP214	psi-mi:“MI:0914”(association)	0.350
CIB2	APAF1	psi-mi:“MI:0914”(association)	0.350

BioGRID (24): RGPD4 (Affinity Capture-MS), RGPD4 (Affinity Capture-MS), RGPD4 (Affinity Capture-MS), RGPD4 (Affinity Capture-MS), RGPD4 (Affinity Capture-MS), RGPD4 (Affinity Capture-MS), RGPD4 (Affinity Capture-MS), RGPD4 (Affinity Capture-MS), RGPD4 (Affinity Capture-MS), RGPD4 (Affinity Capture-MS), RGPD4 (Proximity Label-MS), RGPD4 (Affinity Capture-MS), RGPD5 (Cross-Linking-MS (XL-MS)), RGPD4 (Cross-Linking-MS (XL-MS)), RGPD4 (Cross-Linking-MS (XL-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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	328
Likely benign	38
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

3082 predictions. Top by Δscore:

Variant	Effect	Δscore
2:107836596:TTTTA:T	acceptor_loss	1.0000
2:107836597:TTTAG:T	acceptor_loss	1.0000
2:107836599:TA:T	acceptor_loss	1.0000
2:107836600:A:AG	acceptor_gain	1.0000
2:107836600:A:T	acceptor_loss	1.0000
2:107836601:G:GT	acceptor_gain	1.0000
2:107836601:GA:G	acceptor_gain	1.0000
2:107836601:GAA:G	acceptor_gain	1.0000
2:107836601:GAAGT:G	acceptor_gain	1.0000
2:107836665:AAAAA:A	donor_gain	1.0000
2:107836666:AAAA:A	donor_gain	1.0000
2:107836666:AAAAG:A	donor_loss	1.0000
2:107836667:AAA:A	donor_gain	1.0000
2:107836667:AAAGT:A	donor_loss	1.0000
2:107836668:AA:A	donor_gain	1.0000
2:107836668:AAGT:A	donor_loss	1.0000
2:107836669:AG:A	donor_loss	1.0000
2:107836670:G:GG	donor_gain	1.0000
2:107836670:G:T	donor_loss	1.0000
2:107836671:TAA:T	donor_loss	1.0000
2:107838248:A:AG	acceptor_gain	1.0000
2:107838249:A:G	acceptor_gain	1.0000
2:107838255:A:AG	acceptor_gain	1.0000
2:107838256:G:GG	acceptor_gain	1.0000
2:107838256:GATAC:G	acceptor_gain	1.0000
2:107838365:CAGGG:C	donor_loss	1.0000
2:107838366:AGGGT:A	donor_loss	1.0000
2:107838367:GG:G	donor_gain	1.0000
2:107838368:GG:G	donor_gain	1.0000
2:107838369:G:GA	donor_loss	1.0000

AlphaMissense

11578 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:107859822:T:A	W579R	0.995
2:107859822:T:C	W579R	0.995
2:107859155:T:A	W440R	0.994
2:107859155:T:C	W440R	0.994
2:107859517:T:A	W533R	0.994
2:107859517:T:C	W533R	0.994
2:107859754:T:A	V556D	0.994
2:107860814:A:C	S603R	0.994
2:107860816:T:A	S603R	0.994
2:107860816:T:G	S603R	0.994
2:107859514:T:A	W532R	0.993
2:107859514:T:C	W532R	0.993
2:107861324:T:C	L684P	0.992
2:107854634:A:C	S353R	0.991
2:107854636:C:A	S353R	0.991
2:107854636:C:G	S353R	0.991
2:107859287:G:C	D484H	0.991
2:107859291:T:C	L485P	0.991
2:107859386:T:C	L489P	0.991
2:107859391:G:A	G491R	0.991
2:107859391:G:C	G491R	0.991
2:107859835:T:C	L583P	0.991
2:107861691:T:C	L719P	0.991
2:107859210:T:C	L458P	0.990
2:107859276:T:A	I480K	0.990
2:107860813:A:C	R602S	0.990
2:107860813:A:T	R602S	0.990
2:107859288:A:C	D484A	0.989
2:107843210:T:A	W203R	0.988
2:107843210:T:C	W203R	0.988

dbSNP variants (sampled 300 via entrez): RS1000017831 (2:107836132 G>A), RS1000018256 (2:107855354 C>T), RS1000149172 (2:107845544 G>A,C,T), RS1000194393 (2:107887923 T>A,C), RS1000203318 (2:107845123 C>T), RS1000453093 (2:107855537 C>T), RS1000476870 (2:107831670 G>A,T), RS1000600839 (2:107825016 T>C), RS1000607198 (2:107884582 T>A,G), RS1000733399 (2:107878506 A>G), RS1000804820 (2:107879656 G>A), RS1000849302 (2:107832049 T>C), RS1000879929 (2:107861934 G>A,T), RS1001039938 (2:107884877 G>A), RS1001053886 (2:107854049 C>G)

Disease associations

OMIM: gene MIM:612707 | 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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	increases expression, affects cotreatment	1
Plant Extracts	affects cotreatment, increases expression	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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