RUSC1

gene
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Also known as NESCA

Summary

RUSC1 (RUN and SH3 domain containing 1, HGNC:17153) is a protein-coding gene on chromosome 1q22, encoding AP-4 complex accessory subunit RUSC1 (Q9BVN2). Associates with the adapter-like complex 4 (AP-4) and may therefore play a role in vesicular trafficking of proteins at the trans-Golgi network.

Predicted to enable actin binding activity. Involved in protein polyubiquitination. Located in cytosol.

Source: NCBI Gene 23623 — RefSeq curated summary.

At a glance

  • GWAS associations: 16
  • Clinical variants (ClinVar): 61 total
  • MANE Select transcript: NM_001105203

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17153
Approved symbolRUSC1
NameRUN and SH3 domain containing 1
Location1q22
Locus typegene with protein product
StatusApproved
AliasesNESCA
Ensembl geneENSG00000160753
Ensembl biotypeprotein_coding
OMIM617318
Entrez23623

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 18 protein_coding, 4 retained_intron, 2 nonsense_mediated_decay

ENST00000292254, ENST00000368347, ENST00000368349, ENST00000368352, ENST00000368354, ENST00000462780, ENST00000467820, ENST00000468764, ENST00000471876, ENST00000473331, ENST00000479924, ENST00000485924, ENST00000489860, ENST00000490373, ENST00000492536, ENST00000497930, ENST00000696599, ENST00000878373, ENST00000878374, ENST00000878375, ENST00000878376, ENST00000878377, ENST00000925571, ENST00000955292

RefSeq mRNA: 8 — MANE Select: NM_001105203 NM_001105203, NM_001105204, NM_001105205, NM_001278227, NM_001278228, NM_001278229, NM_001278230, NM_014328

CCDS: CCDS1112, CCDS41410, CCDS41411, CCDS41412

Canonical transcript exons

ENST00000368352 — 10 exons

ExonStartEnd
ENSE00001910161155326580155327132
ENSE00003472217155325864155325910
ENSE00003563846155324845155324943
ENSE00003589081155325316155325490
ENSE00003621075155325567155325672
ENSE00003634623155325102155325178
ENSE00003967800155321688155323130
ENSE00003967804155330403155331114
ENSE00003967807155328150155328275
ENSE00003967810155320894155320991

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 97.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.3061 / max 1222.7925, expressed in 1810 samples.

FANTOM5 promoters (17 alternative TSS)

Promoter IDTPM avgSamples expressed
561719.16741760
56034.9686863
56101.3385936
56190.9410523
56110.8778412
56080.4515255
56020.3320114
56090.292795
56180.178773
56140.168032

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489097.25gold quality
cortical plateUBERON:000534396.98gold quality
cerebellar hemisphereUBERON:000224596.89gold quality
cerebellar cortexUBERON:000212996.82gold quality
cerebellumUBERON:000203796.18gold quality
mucosa of transverse colonUBERON:000499195.74gold quality
right frontal lobeUBERON:000281095.50gold quality
ganglionic eminenceUBERON:000402394.64gold quality
Brodmann (1909) area 10UBERON:001354194.44gold quality
lower esophagus mucosaUBERON:003583494.36gold quality
ileal mucosaUBERON:000033194.18gold quality
prefrontal cortexUBERON:000045194.07gold quality
frontal cortexUBERON:000187093.82gold quality
neocortexUBERON:000195093.67gold quality
paraflocculusUBERON:000535193.60gold quality
cervix squamous epitheliumUBERON:000692293.53gold quality
right coronary arteryUBERON:000162593.42gold quality
Brodmann (1909) area 9UBERON:001354093.41gold quality
cingulate cortexUBERON:000302793.33gold quality
descending thoracic aortaUBERON:000234593.31gold quality
anterior cingulate cortexUBERON:000983593.26gold quality
thoracic aortaUBERON:000151593.25gold quality
ascending aortaUBERON:000149693.24gold quality
frontal poleUBERON:000279593.13gold quality
adenohypophysisUBERON:000219693.09gold quality
esophagus mucosaUBERON:000246993.06gold quality
dorsolateral prefrontal cortexUBERON:000983493.05gold quality
transverse colonUBERON:000115793.00gold quality
middle temporal gyrusUBERON:000277192.96gold quality
hypothalamusUBERON:000189892.88gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.07
E-GEOD-100618no646.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

63 targeting RUSC1, 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-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-4533100.0069.482758
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-12118100.0065.881270
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-318599.9968.121959
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-50799.9770.111915
HSA-MIR-55799.9670.011640
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-427199.8868.322244
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-3065-3P99.8770.251407
HSA-MIR-477999.8666.501583
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-3913-5P99.7867.26968
HSA-MIR-62399.7668.161170
HSA-MIR-3680-3P99.7572.513095
HSA-MIR-2116-3P99.7464.32889

Literature-anchored findings (GeneRIF, showing 6)

  • Data show that NESCA and NEMO interact by their N-terminal region, that NESCA directly associates with TRAF6, which in turn catalyzes NESCA polyubiquitination, and that NESCA overexpression strongly inhibits TRAF6-mediated polyubiquitination of NEMO. (PMID:19365808)
  • Nesca functions as an adapter involved in neuronal vesicular transport (PMID:22404429)
  • RUN domain of NESCA can bind H-Ras, a downstream signaling molecule of TrkA, with high affinity. Moreover, NESCA RUN can directly interact with TrkA. (PMID:22821014)
  • AP-4 deficiency causes missorting of ATG9A in diverse cell types, including patient-derived cells, as well as dysregulation of autophagy. (PMID:30262884)
  • The present study demonstrated that lncRNA RUSC1ASN promoted cell viability and metastasis via Wnt/betacatenin signaling in human breast cancer. (PMID:30569097)
  • LncRNA RUSC1-AS1 promotes osteosarcoma progression through regulating the miR-340-5p and PI3K/AKT pathway. (PMID:34048366)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriorusc1ENSDARG00000078125
mus_musculusRusc1ENSMUSG00000041263
rattus_norvegicusFdpsENSRNOG00000043377

Paralogs (1): RUSC2 (ENSG00000198853)

Protein

Protein identifiers

AP-4 complex accessory subunit RUSC1Q9BVN2 (reviewed: Q9BVN2)

Alternative names: New molecule containing SH3 at the carboxy-terminus, RUN and SH3 domain-containing protein 1

All UniProt accessions (9): Q9BVN2, A0A087WVK5, A0A087WW20, A0A087WX95, A0A087WYB2, A0A087WYU8, A0A087WZ68, A0A8Q3SIT1, Q68CX2

UniProt curated annotations — full annotation on UniProt →

Function. Associates with the adapter-like complex 4 (AP-4) and may therefore play a role in vesicular trafficking of proteins at the trans-Golgi network. Signaling adapter which plays a role in neuronal differentiation. Involved in regulation of NGF-dependent neurite outgrowth. May play a role in neuronal vesicular trafficking, specifically involving pre-synaptic membrane proteins. Seems to be involved in signaling pathways that are regulated by the prolonged activation of MAPK. Can regulate the polyubiquitination of IKBKG and thus may be involved in regulation of the NF-kappa-B pathway.

Subunit / interactions. Associated component of the adapter-like complex 4 (AP-4). Interacts with IKBKG and TRAF6. Interacts with F-actin, acetylated actin, TUBB3, STX1A, KIF5B and KLC1.

Subcellular location. Cytoplasm. Nucleus. Cytoskeleton. Cytoplasmic vesicle. Early endosome. Postsynaptic density. Golgi apparatus.

Tissue specificity. Predominantly expressed in brain.

Post-translational modifications. Phosphorylated on serine residues following nuclear translocation. Polyubiquitinated; polyubiquitination involves TRAF6.

Domain organisation. The RUN domain is necessary for NGF induced nuclear redistribution.

Isoforms (4)

UniProt IDNamesCanonical?
Q9BVN2-11yes
Q9BVN2-22
Q9BVN2-33
Q9BVN2-44

RefSeq proteins (8): NP_001098673, NP_001098674, NP_001098675, NP_001265156, NP_001265157, NP_001265158, NP_001265159, NP_055143 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001452SH3_domainDomain
IPR004012Run_domDomain
IPR036028SH3-like_dom_sfHomologous_superfamily
IPR037213Run_dom_sfHomologous_superfamily
IPR047341RUN_RUSC1Domain
IPR047343RUSC1_2Family

Pfam: PF02759, PF14604

UniProt features (48 total): helix 12, region of interest 8, compositionally biased region 7, sequence conflict 7, splice variant 3, turn 3, domain 2, sequence variant 2, strand 2, chain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4GIWX-RAY DIFFRACTION2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BVN2-F154.040.19

Functional residue map

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

Mutagenesis-validated functional residues (1):

PositionPhenotype
531abrogates nuclear redistribution.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 158 (showing top): ATF_B, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, CREBP1_Q2, USF_C, PATIL_LIVER_CANCER, CREB_Q4, E4F1_Q6, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_PROTEIN_POLYUBIQUITINATION, ATF3_Q6, chr1q22, GOMF_ACTIN_BINDING, BASAKI_YBX1_TARGETS_UP, DOUGLAS_BMI1_TARGETS_UP

GO Biological Process (1): protein polyubiquitination (GO:0000209)

GO Molecular Function (2): actin binding (GO:0003779), protein binding (GO:0005515)

GO Cellular Component (12): nucleus (GO:0005634), early endosome (GO:0005769), Golgi apparatus (GO:0005794), cytosol (GO:0005829), microtubule (GO:0005874), postsynaptic density (GO:0014069), microtubule cytoskeleton (GO:0015630), cytoplasmic vesicle (GO:0031410), cytoplasm (GO:0005737), endosome (GO:0005768), cytoskeleton (GO:0005856), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm3
intracellular membrane-bounded organelle2
endomembrane system2
cellular anatomical structure2
protein ubiquitination1
cytoskeletal protein binding1
binding1
endosome1
microtubule cytoskeleton1
polymeric cytoskeletal fiber1
asymmetric synapse1
postsynaptic specialization1
cytoskeleton1
intracellular vesicle1
intracellular anatomical structure1
cytoplasmic vesicle1
intracellular membraneless organelle1
cell junction1

Protein interactions and networks

STRING

1714 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RUSC1RUNDC3AQ59EK9793
RUSC1SERINC1Q9NRX5594
RUSC1AP4E1Q9UPM8521
RUSC1ATG9AQ7Z3C6519
RUSC1SERINC3Q13530516
RUSC1RUFY1Q96T51473
RUSC1CREBL2O60519456
RUSC1AP4S1Q9Y587430
RUSC1RUBCNQ92622426
RUSC1ACBD4Q8NC06421
RUSC1KREMEN2Q8NCW0419
RUSC1RUFY3Q7L099419
RUSC1TEPSINQ96N21417
RUSC1METRNQ9UJH8415
RUSC1APBA2Q99767407

IntAct

305 interactions, top by confidence:

ABTypeScore
PNMA1RUSC1psi-mi:“MI:0915”(physical association)0.790
RUSC1PNMA1psi-mi:“MI:0915”(physical association)0.790
RUSC1FAM9Bpsi-mi:“MI:0915”(physical association)0.670
RBPMSRUSC1psi-mi:“MI:0915”(physical association)0.670
RUSC1RBPMSpsi-mi:“MI:0915”(physical association)0.670
FAM9BRUSC1psi-mi:“MI:0915”(physical association)0.670
NUDT22RUSC1psi-mi:“MI:0915”(physical association)0.600
WWP2RUSC1psi-mi:“MI:0915”(physical association)0.560
STUB1RUSC1psi-mi:“MI:0915”(physical association)0.560
RUSC1STUB1psi-mi:“MI:0915”(physical association)0.560
RUSC1ZNF620psi-mi:“MI:0915”(physical association)0.560
TBC1D25RUSC1psi-mi:“MI:0915”(physical association)0.560
MAGEA3RUSC1psi-mi:“MI:0915”(physical association)0.560
MAGEA6RUSC1psi-mi:“MI:0915”(physical association)0.560
CTAG1ARUSC1psi-mi:“MI:0915”(physical association)0.560
RBPMSRUSC1psi-mi:“MI:0915”(physical association)0.560
EXOSC8RUSC1psi-mi:“MI:0915”(physical association)0.560

BioGRID (108): RUSC1 (Two-hybrid), RUSC1 (Two-hybrid), RUSC1 (Two-hybrid), RUSC1 (Two-hybrid), FAM9B (Two-hybrid), RUSC1 (Two-hybrid), RUSC1 (Affinity Capture-MS), RUSC1 (Affinity Capture-MS), RUSC1 (Affinity Capture-MS), RUSC1 (Affinity Capture-MS), RUSC1 (Affinity Capture-MS), RUSC1 (Affinity Capture-RNA), RUSC1 (Affinity Capture-MS), RUSC1 (Two-hybrid), RUSC1 (Two-hybrid)

ESM2 similar proteins: A0A1B0GUS0, A0A5F9ZHS7, A7E346, A7MB34, A8MZG2, B2RU40, D4A9R4, O08574, O75593, P0C1Z6, P0CG20, Q0VG99, Q0ZCJ7, Q17QH7, Q29RM2, Q2KIS6, Q2M2S6, Q2M3G4, Q2NL68, Q32LE6, Q3U1J1, Q5JXC2, Q5R815, Q5SW24, Q61660, Q63247, Q6NZ36, Q6PBC9, Q6ZN01, Q6ZRI6, Q7TN08, Q7Z591, Q80VF6, Q86WR7, Q8BG26, Q8BP99, Q8BXQ8, Q8IYS4, Q8N9Y4, Q8NAV2

Diamond homologs: A4FU49, A5D7F8, A5D8S5, A6QLK6, A7E3N7, B1V8A0, D3ZG83, E2RP94, E7F1U2, F1LRS8, G5EC32, M0R4F8, O35413, O35964, O42287, O42854, O43586, O60504, O70145, O89100, O94875, P0CR78, P0CR79, P10569, P19878, P34258, P38753, P62484, P97306, Q07840, Q09822, Q10199, Q13588, Q15811, Q28E95, Q2KJA1, Q3B7M5, Q3UTJ2, Q4R729, Q5HYK7

SIGNOR signaling

3 interactions.

AEffectBMechanism
TRAF6“down-regulates quantity by destabilization”RUSC1polyubiquitination
RUSC1“up-regulates quantity by stabilization”IKBKG
RUSC1up-regulatesNeurite_outgrowthbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance46
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1052 predictions. Top by Δscore:

VariantEffectΔscore
1:155325389:A:AGacceptor_gain1.0000
1:155325389:AC:Aacceptor_gain1.0000
1:155325390:C:CAacceptor_gain1.0000
1:155325395:T:TAacceptor_gain1.0000
1:155325486:GCCAG:Gdonor_gain1.0000
1:155325487:CCAGG:Cdonor_loss1.0000
1:155325488:CAGGT:Cdonor_loss1.0000
1:155325489:AGGT:Adonor_loss1.0000
1:155325491:GT:Gdonor_loss1.0000
1:155325901:G:GTdonor_gain1.0000
1:155328144:TTTTA:Tacceptor_loss1.0000
1:155328145:TTTA:Tacceptor_loss1.0000
1:155328147:TA:Tacceptor_loss1.0000
1:155328147:TAGGA:Tacceptor_gain1.0000
1:155328148:A:ACacceptor_loss1.0000
1:155328148:A:AGacceptor_gain1.0000
1:155328148:AG:Aacceptor_gain1.0000
1:155328148:AGGAG:Aacceptor_gain1.0000
1:155328149:G:GAacceptor_loss1.0000
1:155328149:G:GGacceptor_gain1.0000
1:155328149:GG:Gacceptor_gain1.0000
1:155328149:GGA:Gacceptor_gain1.0000
1:155328273:TAGGT:Tdonor_loss1.0000
1:155328274:AGG:Adonor_loss1.0000
1:155328275:GGT:Gdonor_loss1.0000
1:155328276:GTA:Gdonor_loss1.0000
1:155328277:T:Adonor_loss1.0000
1:155325097:CCCA:Cacceptor_loss0.9900
1:155325099:CA:Cacceptor_loss0.9900
1:155325100:A:AGacceptor_gain0.9900

AlphaMissense

5781 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:155325129:T:AV495D0.998
1:155325149:T:CF502L0.998
1:155325151:C:AF502L0.998
1:155325151:C:GF502L0.998
1:155325150:T:CF502S0.997
1:155325178:G:CK511N0.997
1:155325178:G:TK511N0.997
1:155325376:T:CC532R0.997
1:155325666:T:CL603P0.997
1:155330456:T:CF865S0.997
1:155325359:T:CL526P0.996
1:155325386:T:CL535P0.996
1:155325669:T:CL604P0.996
1:155325883:T:AW612R0.995
1:155325883:T:CW612R0.995
1:155326688:T:CL657P0.995
1:155326693:T:CF659L0.995
1:155326695:C:AF659L0.995
1:155326695:C:GF659L0.995
1:155321808:T:CL12P0.994
1:155325117:T:AV491D0.994
1:155325138:T:GI498S0.994
1:155325374:T:CL531P0.994
1:155325386:T:AL535H0.994
1:155325669:T:AL604H0.994
1:155326670:T:CL651P0.994
1:155326694:T:CF659S0.994
1:155326700:T:CL661P0.994
1:155330455:T:CF865L0.994
1:155330457:C:AF865L0.994

dbSNP variants (sampled 300 via entrez): RS1000097114 (1:155328571 A>T), RS1000146031 (1:155328755 C>A,T), RS1001299987 (1:155328994 A>C), RS1001401431 (1:155329037 T>C), RS1001674000 (1:155328809 G>A,T), RS1002277075 (1:155328033 C>A), RS1003629295 (1:155330447 A>G), RS1003785765 (1:155323970 G>A), RS1003836399 (1:155324261 G>C), RS1004543884 (1:155331335 G>A), RS1004822135 (1:155324474 C>A,T), RS1005415302 (1:155323723 G>C), RS1005426257 (1:155323297 T>A,G), RS1005614574 (1:155327456 A>G), RS1005700122 (1:155323559 C>A,T)

Disease associations

OMIM: gene MIM:617318 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

16 associations (top):

StudyTraitp-value
GCST004131_70Inflammatory bowel disease6.000000e-08
GCST004132_44Crohn’s disease2.000000e-07
GCST007294_124Body fat distribution (trunk fat ratio)8.000000e-35
GCST007294_3Body fat distribution (trunk fat ratio)6.000000e-21
GCST007294_50Body fat distribution (trunk fat ratio)1.000000e-15
GCST007295_17Body fat distribution (leg fat ratio)3.000000e-13
GCST007295_37Body fat distribution (leg fat ratio)7.000000e-17
GCST007295_72Body fat distribution (leg fat ratio)1.000000e-28
GCST010696_19Cortical thickness (min-P)2.000000e-10
GCST010697_10Cortical surface area (min-P)3.000000e-10
GCST010698_59Subcortical volume (min-P)9.000000e-10
GCST010699_20Brain morphology (min-P)7.000000e-10
GCST010700_5Cortical thickness (MOSTest)8.000000e-17
GCST010701_66Cortical surface area (MOSTest)1.000000e-09
GCST010702_43Subcortical volume (MOSTest)3.000000e-10
GCST010703_253Brain morphology (MOSTest)4.000000e-14

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004341body fat distribution
EFO:0004346neuroimaging measurement
EFO:0004840cortical thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs11264359FDPS, RUSC133.751atorvastatin;Bisphosphonates

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation, decreases expression2
Cyclosporinedecreases expression2
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
beta-lapachonedecreases expression1
sodium arsenitedecreases expression1
methacrylaldehydeincreases oxidation, increases abundance, affects cotreatment1
CGP 52608affects binding, increases reaction1
ICG 001increases expression1
bisphenol Saffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, decreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Benzo(a)pyreneaffects methylation1
Cisplatinincreases expression1
Dexamethasoneaffects cotreatment, decreases expression1
Indomethacinaffects cotreatment, decreases expression1
Methyl Methanesulfonateincreases expression1
Ozoneaffects cotreatment, increases oxidation, increases abundance1
Plant Extractsaffects cotreatment, decreases expression1
Smokedecreases expression1
Dronabinolincreases expression1
Tobacco Smoke Pollutionincreases expression1
Valproic Acidaffects expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, decreases expression1
Antirheumatic Agentsincreases expression1
Okadaic Acidincreases expression1
Particulate Matterdecreases expression, increases abundance1
Volatile Organic Compoundsaffects cotreatment, increases oxidation1

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.