ZSWIM8

gene
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Also known as 4832404P21Rik

Summary

ZSWIM8 (zinc finger SWIM-type containing 8, HGNC:23528) is a protein-coding gene on chromosome 10q22.2, encoding Zinc finger SWIM domain-containing protein 8 (A7E2V4). Substrate recognition component of a SCF-like E3 ubiquitin-protein ligase complex that promotes target-directed microRNA degradation (TDMD), a process that mediates degradation of microRNAs (miRNAs).

Enables ubiquitin-like ligase-substrate adaptor activity. Involved in positive regulation of macromolecule metabolic process; protein ubiquitination; and proteolysis involved in protein catabolic process. Part of Cul3-RING ubiquitin ligase complex.

Source: NCBI Gene 23053 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 114 total
  • MANE Select transcript: NM_001367799

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23528
Approved symbolZSWIM8
Namezinc finger SWIM-type containing 8
Location10q22.2
Locus typegene with protein product
StatusApproved
Aliases4832404P21Rik
Ensembl geneENSG00000214655
Ensembl biotypeprotein_coding
OMIM619213
Entrez23053

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 11 protein_coding_CDS_not_defined, 9 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000398706, ENST00000412198, ENST00000425051, ENST00000431225, ENST00000433366, ENST00000446546, ENST00000451629, ENST00000466354, ENST00000466568, ENST00000487278, ENST00000489234, ENST00000492395, ENST00000603114, ENST00000603187, ENST00000603195, ENST00000603309, ENST00000603409, ENST00000603840, ENST00000604165, ENST00000604524, ENST00000604729, ENST00000604754, ENST00000605216

RefSeq mRNA: 4 — MANE Select: NM_001367799 NM_001242487, NM_001242488, NM_001367799, NM_015037

CCDS: CCDS44440, CCDS60560, CCDS91266

Canonical transcript exons

ENST00000604729 — 26 exons

ExonStartEnd
ENSE000015345877379737773797605
ENSE000015346157379454173794639
ENSE000015346467379185973792852
ENSE000015346487379132473791499
ENSE000015346497379097573791176
ENSE000015346517379017273790292
ENSE000015584877378909673789190
ENSE000015593537378936773789539
ENSE000015618307378867073788823
ENSE000034585357379358873793719
ENSE000034598217379414773794330
ENSE000034633487379677473797014
ENSE000034701227379778173798070
ENSE000034776547380001173800170
ENSE000034885647379823073798453
ENSE000034935177378995673790037
ENSE000035242277380101773801195
ENSE000035466747380029673800472
ENSE000035467117379900273799490
ENSE000035697397379711373797271
ENSE000036084437379553973795663
ENSE000036125677379386573794044
ENSE000036379557380131673801793
ENSE000036532667380064073800759
ENSE000036601937378971773789824
ENSE000036760257378560673786086

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 99.26.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.8211 / max 437.8199, expressed in 1817 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
10555020.52481815
1055513.20541512
1055490.090815

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583499.26gold quality
adenohypophysisUBERON:000219699.19gold quality
pituitary glandUBERON:000000798.95gold quality
left testisUBERON:000453398.80gold quality
right testisUBERON:000453498.78gold quality
right lobe of thyroid glandUBERON:000111998.64gold quality
right hemisphere of cerebellumUBERON:001489098.59gold quality
left lobe of thyroid glandUBERON:000112098.49gold quality
right lobe of liverUBERON:000111498.33gold quality
cerebellar hemisphereUBERON:000224598.32gold quality
right adrenal gland cortexUBERON:003582798.32gold quality
metanephros cortexUBERON:001053398.28gold quality
right adrenal glandUBERON:000123398.25gold quality
skin of legUBERON:000151198.24gold quality
esophagogastric junction muscularis propriaUBERON:003584198.21gold quality
cerebellar cortexUBERON:000212998.18gold quality
lower esophagusUBERON:001347398.18gold quality
lower esophagus muscularis layerUBERON:003583398.18gold quality
skin of abdomenUBERON:000141698.13gold quality
muscle layer of sigmoid colonUBERON:003580598.11gold quality
minor salivary glandUBERON:000183098.07gold quality
endocervixUBERON:000045898.02gold quality
ectocervixUBERON:001224998.01gold quality
small intestine Peyer’s patchUBERON:000345497.96gold quality
right frontal lobeUBERON:000281097.95gold quality
left adrenal gland cortexUBERON:003582597.94gold quality
right ovaryUBERON:000211897.89gold quality
left adrenal glandUBERON:000123497.87gold quality
mucosa of stomachUBERON:000119997.85gold quality
right uterine tubeUBERON:000130297.83gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting ZSWIM8, 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-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4455100.0065.481587
HSA-MIR-3605-5P99.9667.12932
HSA-MIR-6512-3P99.6566.071468
HSA-MIR-6720-5P99.6566.221459
HSA-MIR-608399.4768.732393
HSA-MIR-449B-3P99.2067.241047
HSA-MIR-6815-3P99.1368.981530
HSA-MIR-5008-3P98.7367.501433
HSA-MIR-19898.7067.32920
HSA-MIR-7113-5P97.8867.331735
HSA-MIR-227897.3066.191130
HSA-MIR-6849-3P97.2564.571371
HSA-MIR-874-5P96.9363.921014
HSA-MIR-365195.6264.67287
HSA-MIR-6753-5P94.7064.08470

Literature-anchored findings (GeneRIF, showing 4)

  • A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming. (PMID:33184234)
  • The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation. (PMID:33184237)
  • ZSWIM8 is a myogenic protein that partly prevents C2C12 differentiation. (PMID:34686700)
  • The conserved Pelado/ZSWIM8 protein regulates actin dynamics by promoting linear actin filament polymerization. (PMID:35940847)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriozswim8ENSDARG00000069397
mus_musculusZswim8ENSMUSG00000021819
rattus_norvegicusZswim8ENSRNOG00000056617
drosophila_melanogasterDoraFBGN0085430
caenorhabditis_elegansWBGENE00004140

Paralogs (3): ZSWIM6 (ENSG00000130449), ZSWIM4 (ENSG00000132003), ZSWIM5 (ENSG00000162415)

Protein

Protein identifiers

Zinc finger SWIM domain-containing protein 8A7E2V4 (reviewed: A7E2V4)

All UniProt accessions (10): A7E2V4, H0YCW2, H7BZ52, H7C453, S4R393, S4R3B3, S4R3H3, S4R3S6, S4R3U7, S4R410

UniProt curated annotations — full annotation on UniProt →

Function. Substrate recognition component of a SCF-like E3 ubiquitin-protein ligase complex that promotes target-directed microRNA degradation (TDMD), a process that mediates degradation of microRNAs (miRNAs). The SCF-like E3 ubiquitin-protein ligase complex acts by catalyzing ubiquitination and subsequent degradation of AGO proteins (AGO1, AGO2, AGO3 and/or AGO4), thereby exposing miRNAs for degradation. Specifically recognizes and binds AGO proteins when they are engaged with a TDMD target. May also act as a regulator of axon guidance: specifically recognizes misfolded ROBO3 and promotes its ubiquitination and subsequent degradation. Plays an essential role for proper embryonic development of heart and lung. Controls protein quality of DAB1, a key signal molecule for brain development, thus protecting its signaling strength. Mechanistically, recognizes intrinsically disordered regions of DAB1 and eliminates misfolded DAB1 that cannot be properly phosphorylated. (Microbial infection) Participates in Zika virus inhibition of IFN signaling by acting as a scaffold protein to connect ZSWIM8/CUL3 ligase complex and STAT2, leading to STAT2 degradation.

Subunit / interactions. Component of the SCF-like E3 ubiquitin-protein ligase complex which contains CUL3, RBX1, ELOB, ELOC and ZSWIM8. (Microbial infection) Interacts with Zika virus protein NS5; this interaction allows STAT2 binding and subsequent proteasomal degradation.

Subcellular location. Cytoplasm. Cytosol.

Pathway. Protein modification; protein ubiquitination.

Similarity. Belongs to the ZSWIM8 family.

Isoforms (5)

UniProt IDNamesCanonical?
A7E2V4-11yes
A7E2V4-22
A7E2V4-33
A7E2V4-44
A7E2V4-55

RefSeq proteins (4): NP_001229416, NP_001229417, NP_001354728, NP_055852 (=MANE)

Domains & families (InterPro)

IDNameType
IPR007527Znf_SWIMDomain
IPR048370ZSWIM4-8_CDomain
IPR057945TPR_ZSWIM8Domain

Pfam: PF21055, PF25572

UniProt features (43 total): modified residue 11, compositionally biased region 10, sequence conflict 10, region of interest 6, splice variant 4, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
9RWZELECTRON MICROSCOPY3.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A7E2V4-F163.330.29

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 (11): 36, 48, 53, 437, 567, 1139, 1153, 1156, 1160, 1267, 1836

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-9010553Regulation of expression of SLITs and ROBOs

MSigDB gene sets: 153 (showing top): GOBP_MACROMOLECULE_CATABOLIC_PROCESS, AP4_Q6, CAGCTG_AP4_Q5, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, CAIRO_HEPATOBLASTOMA_CLASSES_DN, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, NF1_Q6_01, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, TCF11_01, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, ATF3_Q6, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, HAND1E47_01

GO Biological Process (6): protein quality control for misfolded or incompletely synthesized proteins (GO:0006515), protein ubiquitination (GO:0016567), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), target-directed miRNA degradation (GO:0140958), positive regulation of miRNA catabolic process (GO:2000627), type I interferon-mediated signaling pathway (GO:0060337)

GO Molecular Function (3): zinc ion binding (GO:0008270), ubiquitin-like ligase-substrate adaptor activity (GO:1990756), metal ion binding (GO:0046872)

GO Cellular Component (5): cytosol (GO:0005829), Cul2-RING ubiquitin ligase complex (GO:0031462), Cul3-RING ubiquitin ligase complex (GO:0031463), cytoplasm (GO:0005737), cullin-RING ubiquitin ligase complex (GO:0031461)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Signaling by ROBO receptors1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
miRNA catabolic process2
cellular anatomical structure2
cullin-RING ubiquitin ligase complex2
protein catabolic process1
protein modification by small protein conjugation1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
post-transcriptional gene silencing1
negative regulation of miRNA-mediated gene silencing1
positive regulation of catabolic process1
regulation of miRNA catabolic process1
positive regulation of miRNA metabolic process1
cellular response to type I interferon1
interferon-mediated signaling pathway1
transition metal ion binding1
enzyme-substrate adaptor activity1
cation binding1
cytoplasm1
intracellular anatomical structure1
ubiquitin ligase complex1

Protein interactions and networks

STRING

845 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZSWIM8MRPS14O60783535
ZSWIM8ZBTB44Q8NCP5528
ZSWIM8CAAP1Q9H8G2513
ZSWIM8CLEC17AQ6ZS10483
ZSWIM8TAF9BQ9HBM6476
ZSWIM8BMS1Q14692475
ZSWIM8DDX52Q9Y2R4474
ZSWIM8SLC39A13Q96H72447
ZSWIM8SLC15A2Q16348433
ZSWIM8CUL2Q13617418
ZSWIM8ZSWIM2Q8NEG5410
ZSWIM8ZNRF2Q8NHG8407
ZSWIM8ECM1Q16610407
ZSWIM8ROBO2Q9HCK4405
ZSWIM8CEACAM1P13688396

IntAct

66 interactions, top by confidence:

ABTypeScore
CSNK1EZSWIM8psi-mi:“MI:0914”(association)0.530
CUL3ZSWIM8psi-mi:“MI:0914”(association)0.530
JPH4ZSWIM8psi-mi:“MI:0914”(association)0.530
ZSWIM8SURF6psi-mi:“MI:0915”(physical association)0.400
ZSWIM8CTDSP1psi-mi:“MI:0915”(physical association)0.370
ZSWIM8SPG11psi-mi:“MI:0915”(physical association)0.370
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
STING1ZSWIM8psi-mi:“MI:0914”(association)0.350
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350
NUAK1ZSWIM8psi-mi:“MI:0914”(association)0.350
CSNK1DTMEM131Lpsi-mi:“MI:0914”(association)0.350
CSNK1G2ZSWIM8psi-mi:“MI:0914”(association)0.350
DYRK2ZSWIM8psi-mi:“MI:0914”(association)0.350
AURKBTARS3psi-mi:“MI:0914”(association)0.350
MAST1ZSWIM8psi-mi:“MI:0914”(association)0.350
ARRDC2ZSWIM8psi-mi:“MI:0914”(association)0.350
TXNIPZSWIM8psi-mi:“MI:0914”(association)0.350
ATG16L1ESYT2psi-mi:“MI:0914”(association)0.350
DUSP16MEIOCpsi-mi:“MI:0914”(association)0.350
RPL15ZSWIM8psi-mi:“MI:0914”(association)0.350
MRPL4ZSWIM8psi-mi:“MI:0914”(association)0.350
OLFM2ZSWIM8psi-mi:“MI:0914”(association)0.350
TULP2ZSWIM8psi-mi:“MI:0914”(association)0.350
ASB3ZSWIM8psi-mi:“MI:0914”(association)0.350
FGF11ZSWIM8psi-mi:“MI:0914”(association)0.350
TSPYL6ZSWIM8psi-mi:“MI:0914”(association)0.350
PRG2ZSWIM8psi-mi:“MI:0914”(association)0.350
SOCS1ZSWIM8psi-mi:“MI:0914”(association)0.350

BioGRID (100): ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Proximity Label-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS), ZSWIM8 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8HBI7, A0A1L8HJK9, A0A1L8HTT5, A6NP61, A7E2V4, B2RVL6, C0SPG1, C3VD30, K7SGN7, P56163, P56198, P62932, Q1XFL1, Q29RJ0, Q32L09, Q3UHH1, Q3V0J4, Q497M3, Q4R739, Q58D79, Q5EA86, Q5R8D5, Q5TKR9, Q5VWQ0, Q5XI33, Q6DMN8, Q768S4, Q7T3T8, Q7T3T9, Q7T3U0, Q80T69, Q8BV79, Q8BZ21, Q8CAK3, Q8CDN1, Q8HXK7, Q8K3Y6, Q8N2G6, Q8N9V6, Q8ND61

Diamond homologs: A7E2V4, A7E305, Q3UHH1, Q80TC6, Q8C7B8, Q9H7M6, Q9P217, Q9VWN9, Q80TB7, Q9HCJ5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance95
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4537 predictions. Top by Δscore:

VariantEffectΔscore
10:73786084:GAGG:Gdonor_loss1.0000
10:73786085:AG:Adonor_loss1.0000
10:73786087:GTGA:Gdonor_loss1.0000
10:73788646:T:TAacceptor_gain1.0000
10:73788657:ATT:Aacceptor_gain1.0000
10:73788659:T:Aacceptor_gain1.0000
10:73788667:A:Gacceptor_gain1.0000
10:73789088:A:AGacceptor_gain1.0000
10:73789089:C:Gacceptor_gain1.0000
10:73789091:CCCAG:Cacceptor_loss1.0000
10:73789092:CCA:Cacceptor_loss1.0000
10:73789094:A:AGacceptor_gain1.0000
10:73789094:A:Tacceptor_loss1.0000
10:73789094:AG:Aacceptor_gain1.0000
10:73789094:AGGCT:Aacceptor_gain1.0000
10:73789095:G:GCacceptor_gain1.0000
10:73789095:GG:Gacceptor_gain1.0000
10:73789095:GGC:Gacceptor_gain1.0000
10:73789095:GGCT:Gacceptor_gain1.0000
10:73789095:GGCTG:Gacceptor_gain1.0000
10:73789186:GATAG:Gdonor_gain1.0000
10:73789187:A:Gdonor_gain1.0000
10:73789187:ATAGG:Adonor_loss1.0000
10:73789189:AGG:Adonor_loss1.0000
10:73789191:G:GGdonor_gain1.0000
10:73789192:T:Gdonor_loss1.0000
10:73789365:AG:Aacceptor_gain1.0000
10:73789366:GG:Gacceptor_gain1.0000
10:73789469:GCT:Gdonor_gain1.0000
10:73789540:G:GGdonor_gain1.0000

AlphaMissense

11838 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:73785924:T:CF16L1.000
10:73785926:C:AF16L1.000
10:73785926:C:GF16L1.000
10:73785942:T:CF22L1.000
10:73785944:T:AF22L1.000
10:73785944:T:GF22L1.000
10:73785999:T:AW41R1.000
10:73785999:T:CW41R1.000
10:73786000:G:CW41S1.000
10:73786001:G:CW41C1.000
10:73786001:G:TW41C1.000
10:73786008:T:AW44R1.000
10:73786008:T:CW44R1.000
10:73786010:G:CW44C1.000
10:73786010:G:TW44C1.000
10:73788688:T:GL76W1.000
10:73788697:T:CL79P1.000
10:73788702:G:CA81P1.000
10:73788724:T:AI88N1.000
10:73788729:T:AF90I1.000
10:73788729:T:CF90L1.000
10:73788730:T:CF90S1.000
10:73788730:T:GF90C1.000
10:73788731:T:AF90L1.000
10:73788731:T:GF90L1.000
10:73788742:A:TE94V1.000
10:73788772:T:CL104P1.000
10:73788778:T:CL106P1.000
10:73788784:T:AI108N1.000
10:73788784:T:GI108S1.000

dbSNP variants (sampled 300 via entrez): RS1000017397 (10:73798973 C>A,T), RS1000035989 (10:73793182 G>A), RS1000108319 (10:73799875 T>C), RS1000176467 (10:73798183 TG>T), RS1000419857 (10:73786457 A>G), RS1001247176 (10:73784802 A>G), RS1001388694 (10:73786625 A>C,G), RS1001635100 (10:73791557 G>A,C,T), RS1001689150 (10:73797237 G>A), RS1001899799 (10:73794014 G>C), RS1002055580 (10:73796219 C>T), RS1002609522 (10:73802195 T>A,C), RS1002907182 (10:73789938 C>T), RS1002923266 (10:73788877 T>G), RS1002958959 (10:73795248 T>C)

Disease associations

OMIM: gene MIM:619213 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST004132_74Crohn’s disease2.000000e-09
GCST007656_13Chronic obstructive pulmonary disease or resting heart rate (pleiotropy)2.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression3
bisphenol Adecreases expression, decreases methylation2
sodium arseniteincreases expression, affects cotreatment, decreases expression, increases abundance2
(+)-JQ1 compoundincreases expression2
Resveratrolaffects cotreatment, decreases expression2
Air Pollutantsaffects expression, increases abundance, increases expression2
aristolochic acid Iincreases expression1
FR900359decreases phosphorylation1
triphenyl phosphateaffects expression1
beta-lapachonedecreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
abrineincreases expression1
Arsenicdecreases expression, increases abundance, affects cotreatment1
Coumestrolaffects cotreatment, decreases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Diurondecreases expression1
Doxorubicindecreases expression1
Folic Acidincreases expression1
Formaldehydedecreases expression1
Manganeseaffects cotreatment, decreases expression, increases abundance1
Mustard Gasincreases expression1
Ozoneaffects expression, increases abundance1
Plant Extractsaffects cotreatment, decreases expression1
Smokedecreases expression1
Dihydrotestosteroneincreases expression1
Urethaneincreases expression1
Antirheumatic Agentsincreases expression1

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.