RANBP10

gene
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Also known as KIAA1464

Summary

RANBP10 (RAN binding protein 10, HGNC:29285) is a protein-coding gene on chromosome 16q22, encoding Ran-binding protein 10 (Q6VN20). May act as an adapter protein to couple membrane receptors to intracellular signaling pathways.

RAN is a small GTPase involved in the assembly of microtubules to form mitotic spindles. The protein encoded by this gene is a cytoplasmic guanine nucleotide exchange factor (GEF) that binds beta-tubulin and has GEF activity toward RAN. The encoded protein plays a role in the formation of noncentrosomal microtubules. In addition, this protein may be involved in the regulation of D(1) receptor signaling by protein kinase C delta and protein kinase C gamma. Several transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 57610 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 102 total
  • MANE Select transcript: NM_020850

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29285
Approved symbolRANBP10
NameRAN binding protein 10
Location16q22
Locus typegene with protein product
StatusApproved
AliasesKIAA1464
Ensembl geneENSG00000141084
Ensembl biotypeprotein_coding
OMIM614031
Entrez57610

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 11 protein_coding, 3 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000317506, ENST00000448631, ENST00000602506, ENST00000602525, ENST00000602638, ENST00000602677, ENST00000602815, ENST00000602887, ENST00000863257, ENST00000863258, ENST00000863259, ENST00000863260, ENST00000924472, ENST00000924473, ENST00000924474, ENST00000942173

RefSeq mRNA: 5 — MANE Select: NM_020850 NM_001320238, NM_001320239, NM_001320240, NM_001410883, NM_020850

CCDS: CCDS32469, CCDS81999, CCDS92180

Canonical transcript exons

ENST00000317506 — 14 exons

ExonStartEnd
ENSE000012375186772307067726558
ENSE000034646166777203467772086
ENSE000034898856772775167727896
ENSE000035229816772928067729484
ENSE000035264166772839067728511
ENSE000035537406772968067729828
ENSE000035551356772993867730046
ENSE000035732296773801367738035
ENSE000036169766780630267806560
ENSE000036268566774428867744455
ENSE000036413416773485867735042
ENSE000036457966773147267731584
ENSE000036779896780542867805539
ENSE000036828816772732767727438

Expression profiles

Bgee: expression breadth ubiquitous, 261 present calls, max score 92.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.5842 / max 799.2251, expressed in 1818 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
15781832.82911818
1578171.7551114

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right uterine tubeUBERON:000130292.50gold quality
right adrenal gland cortexUBERON:003582790.54gold quality
right hemisphere of cerebellumUBERON:001489090.33gold quality
right adrenal glandUBERON:000123390.20gold quality
right lobe of liverUBERON:000111490.06gold quality
cerebellar hemisphereUBERON:000224589.64gold quality
left adrenal glandUBERON:000123489.47gold quality
cerebellar cortexUBERON:000212989.45gold quality
left adrenal gland cortexUBERON:003582589.45gold quality
adrenal cortexUBERON:000123588.87gold quality
gastrocnemiusUBERON:000138888.50gold quality
cerebellumUBERON:000203788.02gold quality
adrenal glandUBERON:000236987.89gold quality
lower esophagus mucosaUBERON:003583487.86gold quality
muscle of legUBERON:000138387.59gold quality
hindlimb stylopod muscleUBERON:000425286.93gold quality
left ovaryUBERON:000211985.65gold quality
body of uterusUBERON:000985385.29gold quality
bloodUBERON:000017885.21gold quality
ectocervixUBERON:001224985.19gold quality
right ovaryUBERON:000211885.12gold quality
endocervixUBERON:000045884.87gold quality
skin of legUBERON:000151184.79gold quality
trabecular bone tissueUBERON:000248384.61gold quality
skin of abdomenUBERON:000141684.55gold quality
metanephros cortexUBERON:001053384.46gold quality
body of pancreasUBERON:000115084.42gold quality
granulocyteCL:000009484.40gold quality
tendon of biceps brachiiUBERON:000818884.03silver quality
pancreatic ductal cellCL:000207983.97gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes3.67
E-GEOD-100618no243.26

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): YY1

miRNA regulators (miRDB)

149 targeting RANBP10, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-4533100.0069.482758
HSA-MIR-4673100.0066.641490
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-4692100.0067.322066
HSA-MIR-5692A100.0074.406850
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-5193100.0067.261744
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-451499.9967.101870
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-373-5P99.9875.364753
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-426799.9666.532368
HSA-MIR-6825-5P99.9669.813431

Literature-anchored findings (GeneRIF, showing 6)

  • RanBP10 might serve as a molecular link between Ran and noncentrosomal microtubules (PMID:18347012)
  • data support the idea that RanBP9 and RanBP10 may function as signaling integrators and dictate the efficient regulation of D(1) receptor signaling by PKCdelta and PKCgamma (PMID:20395553)
  • The results showed that ICP0 interacted with cell protein RanBP10, a known transcriptional coactivator, in human herpesvirus 1-infected cells. (PMID:26739050)
  • Authors provide evidence that enhancement of neuronal morphology through RANBP10 is one of the neuroprotective mechanisms for miR-196a. (PMID:28744327)
  • A Ran-binding protein facilitates nuclear import of human papillomavirus type 16. (PMID:33974675)
  • RANBP10 promotes glioblastoma progression by regulating the FBXW7/c-Myc pathway. (PMID:34671019)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioranbp10ENSDARG00000062138
mus_musculusRanbp10ENSMUSG00000037415
rattus_norvegicusRanbp10ENSRNOG00000018000
drosophila_melanogasterRanBPMFBGN0262114

Paralogs (3): RANBP9 (ENSG00000010017), GID8 (ENSG00000101193), SPRYD3 (ENSG00000167778)

Protein

Protein identifiers

Ran-binding protein 10Q6VN20 (reviewed: Q6VN20)

All UniProt accessions (5): Q6VN20, R4GMX7, R4GMX8, R4GN91, R4GNA3

UniProt curated annotations — full annotation on UniProt →

Function. May act as an adapter protein to couple membrane receptors to intracellular signaling pathways. Core component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1. Enhances dihydrotestosterone-induced transactivation activity of AR, as well as dexamethasone-induced transactivation activity of NR3C1, but does not affect estrogen-induced transactivation. Acts as a guanine nucleotide exchange factor (GEF) for RAN GTPase. May play an essential role in hemostasis and in maintaining microtubule dynamics with respect to both platelet shape and function.

Subunit / interactions. May form homodimers. Identified in the CTLH complex that contains GID4, RANBP9 and/or RANBP10, MKLN1, MAEA, RMND5A (or alternatively its paralog RMND5B), GID8, ARMC8, WDR26 and YPEL5. Within this complex, MAEA, RMND5A (or alternatively its paralog RMND5B), GID8, WDR26, and RANBP9 and/or RANBP10 form the catalytic core, while GID4, MKLN1, ARMC8 and YPEL5 have ancillary roles. Interacts with RAN and RANBP9. Interacts with the HGF receptor MET. Interacts with AR. Interacts with TUBB1. Interacts with YPEL5. May interact with TUBB5. Interacts with DDX4.

Subcellular location. Cytoplasm. Cytosol. Nucleus.

Tissue specificity. Broadly expressed, with highest levels in skeletal muscle.

Domain organisation. The SPRY domain mediates the interaction with MET.

Similarity. Belongs to the RANBP9/10 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q6VN20-11yes
Q6VN20-22
Q6VN20-33

RefSeq proteins (5): NP_001307167, NP_001307168, NP_001307169, NP_001397812, NP_065901* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001870B30.2/SPRYDomain
IPR003877SPRY_domDomain
IPR006594LisHConserved_site
IPR006595CTLH_CDomain
IPR013144CRA_domDomain
IPR013320ConA-like_dom_sfHomologous_superfamily
IPR024964CTLH/CRADomain
IPR035782SPRY_RanBP9/10Domain
IPR043136B30.2/SPRY_sfHomologous_superfamily
IPR050618Ubq-SigPath_RegFamily

Pfam: PF00622, PF08513, PF10607

UniProt features (24 total): modified residue 9, splice variant 3, domain 3, compositionally biased region 3, sequence conflict 2, region of interest 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6VN20-F178.140.60

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 (9): 2, 361, 362, 365, 367, 369, 422, 451, 453

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-8851805MET activates RAS signaling

MSigDB gene sets: 245 (showing top): CREL_01, ACTACCT_MIR196A_MIR196B, chr16q22, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, AACYNNNNTTCCS_UNKNOWN, TGACCTY_ERR1_Q2, FOXO4_01, GOMF_GTPASE_BINDING, GGAMTNNNNNTCCY_UNKNOWN, SP1_Q2_01, GNF2_ANK1, GTGCCTT_MIR506, NFKB_C, GNF2_SPTA1, FONTAINE_PAPILLARY_THYROID_CARCINOMA_DN

GO Biological Process (2): microtubule cytoskeleton organization (GO:0000226), cytoskeleton organization (GO:0007010)

GO Molecular Function (4): guanyl-nucleotide exchange factor activity (GO:0005085), small GTPase binding (GO:0031267), beta-tubulin binding (GO:0048487), protein binding (GO:0005515)

GO Cellular Component (5): ubiquitin ligase complex (GO:0000151), nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), microtubule cytoskeleton (GO:0015630)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Signaling by MET1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
cytoskeleton organization1
microtubule-based process1
organelle organization1
GTP binding1
GDP binding1
GTPase regulator activity1
GTPase binding1
tubulin binding1
binding1
intracellular protein-containing complex1
transferase complex1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1
cytoskeleton1

Protein interactions and networks

STRING

1234 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RANBP10MKLN1Q9UL63843
RANBP10YPEL5P62699839
RANBP10GID4Q8IVV7812
RANBP10ARMC8Q8IUR7804
RANBP10WDR26Q9H7D7783
RANBP10RMND5AQ9H871731
RANBP10GID8Q9NWU2727
RANBP10RMND5BQ96G75716
RANBP10MAEAQ7L5Y9707
RANBP10TUBBP05218610
RANBP10RANBP3Q9H6Z4525
RANBP10UBE2HP37286444
RANBP10RANBP1P43487444
RANBP10RAB40ALP0C0E4431
RANBP10NACC1Q96RE7429
RANBP10LRIF1Q5T3J3429

IntAct

176 interactions, top by confidence:

ABTypeScore
ARMC8HTRA2psi-mi:“MI:0914”(association)0.750
CCDC120AIPpsi-mi:“MI:0914”(association)0.640
CRIPTOAIPpsi-mi:“MI:0914”(association)0.640
NDUFS6NDUFS8psi-mi:“MI:0914”(association)0.640
RANBP10MAEApsi-mi:“MI:0914”(association)0.640
PRG2YPEL5psi-mi:“MI:0914”(association)0.640
INAVACYTH3psi-mi:“MI:0914”(association)0.640
GID8HTRA2psi-mi:“MI:0914”(association)0.610
MAGEA11RANBP10psi-mi:“MI:0915”(physical association)0.560
CTAG1ARANBP10psi-mi:“MI:0915”(physical association)0.560
IGFBP6RANBP10psi-mi:“MI:0915”(physical association)0.560
INSL6POTEFpsi-mi:“MI:0914”(association)0.530
PRG3ZNF324psi-mi:“MI:0914”(association)0.530
PIGTZNF609psi-mi:“MI:0914”(association)0.530
PRICKLE3SIAH2psi-mi:“MI:0914”(association)0.530
BMP1TLL1psi-mi:“MI:0914”(association)0.530
MRPL38DUSP14psi-mi:“MI:0914”(association)0.530
NME1NME2P1psi-mi:“MI:0914”(association)0.530
JPH4ZSWIM8psi-mi:“MI:0914”(association)0.530
TIGD5P4HA2psi-mi:“MI:0914”(association)0.530
EMILIN3ZZEF1psi-mi:“MI:0914”(association)0.530

BioGRID (177): RANBP10 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP10 (Co-fractionation), WDR26 (Co-fractionation), RANBP10 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS)

ESM2 similar proteins: A0JMA8, A1A5P5, A1L252, A1YVX4, A3KMI0, A3KMV8, A6H8H2, F4HYD7, F4HYJ7, O73630, O94712, P29375, P41229, P41230, P69566, Q04861, Q1LUS8, Q28FM1, Q30DN6, Q32SG6, Q38JA7, Q3B8D5, Q3UXZ9, Q4R8E0, Q5F3R2, Q5U245, Q5VZ89, Q5XUN4, Q62240, Q63185, Q6IQX0, Q6P158, Q6P5D3, Q6VN19, Q6VN20, Q7Z3E5, Q7Z401, Q80Y84, Q94545, Q96S59

Diamond homologs: A1CNW8, A1D1S7, A1L252, A3KMV8, A6S3E0, A6ZZJ6, A7EQ00, A7TE03, O74497, O94712, P18160, P32343, P69566, Q03212, Q1E2D2, Q1LUS8, Q28FM1, Q4WRW0, Q4Z8K6, Q5RBR6, Q6BSU1, Q6FJG2, Q6VN19, Q6VN20, Q8NCJ5, Q96S59, Q96UB6, Q9PTY5, A0A5F9C6I2, D3ZXK7, F4HYD7, P53076, Q19614, Q54X16, Q5XPI3, Q5XPI4, Q84WK5, Q9C8J7, Q9SIZ8, Q5XH91

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 167 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.

Reactome pathways:

PathwayPartnersFoldFDR
Regulation of pyruvate metabolism1050.1×8e-13
Pyruvate metabolism517.9×3e-03

GO biological processes:

GO termPartnersFoldFDR
proteasome-mediated ubiquitin-dependent protein catabolic process134.6×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance77
Likely benign5
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

3039 predictions. Top by Δscore:

VariantEffectΔscore
16:67727742:AT:Adonor_gain1.0000
16:67727743:T:TAdonor_gain1.0000
16:67727745:CTGTA:Cdonor_loss1.0000
16:67727746:TGTA:Tdonor_loss1.0000
16:67727747:GTAC:Gdonor_loss1.0000
16:67727748:TA:Tdonor_loss1.0000
16:67727749:A:AGdonor_loss1.0000
16:67727750:CCT:Cdonor_loss1.0000
16:67727789:C:CAdonor_gain1.0000
16:67727809:AATG:Adonor_gain1.0000
16:67727904:C:CTacceptor_gain1.0000
16:67727911:C:Tacceptor_gain1.0000
16:67728385:CTCAC:Cdonor_loss1.0000
16:67728386:TCA:Tdonor_loss1.0000
16:67728387:CA:Cdonor_loss1.0000
16:67728388:AC:Adonor_gain1.0000
16:67728389:CC:Cdonor_gain1.0000
16:67728389:CCCA:Cdonor_loss1.0000
16:67728403:AT:Adonor_gain1.0000
16:67728510:CG:Cacceptor_gain1.0000
16:67728512:C:CCacceptor_gain1.0000
16:67729483:TCCTA:Tacceptor_loss1.0000
16:67729484:CCTAG:Cacceptor_loss1.0000
16:67729748:T:TAdonor_gain1.0000
16:67729826:CAC:Cacceptor_gain1.0000
16:67729827:ACCT:Aacceptor_loss1.0000
16:67729829:C:CCacceptor_gain1.0000
16:67729829:CTGT:Cacceptor_loss1.0000
16:67729830:T:Aacceptor_loss1.0000
16:67729934:TTAC:Tdonor_loss1.0000

AlphaMissense

4082 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:67727344:A:GL572P1.000
16:67727425:A:GL545P1.000
16:67729817:A:GF337S1.000
16:67729941:A:GL332P1.000
16:67731476:T:AR295S1.000
16:67731476:T:GR295S1.000
16:67731567:A:GL265P1.000
16:67734968:G:CF222L1.000
16:67734968:G:TF222L1.000
16:67734969:A:GF222S1.000
16:67734970:A:CF222V1.000
16:67734970:A:GF222L1.000
16:67734970:A:TF222I1.000
16:67734981:C:AG218V1.000
16:67734981:C:TG218E1.000
16:67734983:A:CF217L1.000
16:67734983:A:TF217L1.000
16:67734984:A:CF217C1.000
16:67734984:A:GF217S1.000
16:67734985:A:GF217L1.000
16:67734986:G:CN216K1.000
16:67734986:G:TN216K1.000
16:67735002:T:AE211V1.000
16:67735003:C:TE211K1.000
16:67735011:G:AT208I1.000
16:67735013:C:AQ207H1.000
16:67735013:C:GQ207H1.000
16:67735014:T:GQ207P1.000
16:67735017:A:GL206P1.000
16:67735017:A:TL206Q1.000

dbSNP variants (sampled 300 via entrez): RS1000004764 (16:67736109 C>T), RS1000013726 (16:67769897 C>T), RS1000051477 (16:67805252 G>C), RS1000061138 (16:67767581 G>A), RS1000063364 (16:67799125 G>A), RS1000071685 (16:67749060 C>T), RS1000087109 (16:67732615 A>G), RS1000103529 (16:67804846 T>A,G), RS1000118081 (16:67745615 G>A), RS1000139784 (16:67732914 C>T), RS1000222238 (16:67785450 C>T), RS1000239122 (16:67779502 T>A), RS1000250912 (16:67794368 C>T), RS1000259981 (16:67725487 A>G), RS1000278167 (16:67729799 C>G)

Disease associations

OMIM: gene MIM:614031 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST002539_84Schizophrenia2.000000e-08
GCST002899_33HDL cholesterol9.000000e-26
GCST004604_73Hematocrit4.000000e-11
GCST004615_105Hemoglobin concentration2.000000e-11
GCST005751_4Empathy quotient9.000000e-07
GCST006803_42Schizophrenia4.000000e-08
GCST010002_113Refractive error2.000000e-14
GCST90002383_245Hematocrit3.000000e-27
GCST90020029_574Waist circumference adjusted for body mass index2.000000e-09

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004348hematocrit
EFO:0004509hemoglobin measurement
EFO:0009183empathy measurement
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

ChemicalActions (top 5)PubMed papers
cobaltous chlorideincreases expression2
Benzo(a)pyrenedecreases expression, decreases methylation2
aristolochic acid Iincreases expression1
FR900359increases phosphorylation1
dicrotophosincreases expression1
bisphenol Adecreases expression1
beta-lapachonedecreases expression, increases expression1
sodium arseniteincreases abundance, increases expression1
beta-methylcholineaffects expression1
CGP 52608affects binding, increases reaction1
ICG 001decreases expression1
abrineincreases expression1
Sunitinibincreases expression1
Acetaminophenincreases expression1
Arsenicincreases abundance, increases expression1
Caffeineincreases phosphorylation1
Ethyl Methanesulfonateincreases expression1
Methyl Methanesulfonateincreases expression1
Quercetinincreases expression1
Ribonucleotidesaffects binding1
Rotenoneincreases expression1
Cyclosporinedecreases expression1
Aflatoxin B1affects expression1
Antirheumatic Agentsincreases expression1
Okadaic Aciddecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B2DCAbcam HeLa RANBP10 KOCancer cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.