SPSB3

gene
On this page

Also known as SSB-3

Summary

SPSB3 (splA/ryanodine receptor domain and SOCS box containing 3, HGNC:30629) is a protein-coding gene on chromosome 16p13.3, encoding SPRY domain-containing SOCS box protein 3 (Q6PJ21). Substrate-recognition component of a cullin-5-RING E3 ubiquitin-protein ligase complex (ECS complex, also named CRL5 complex), which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as CGAS and SNAI1.

Enables ubiquitin-like ligase-substrate adaptor activity. Involved in several processes, including negative regulation of cGAS/STING signaling pathway; negative regulation of epithelial to mesenchymal transition; and protein K48-linked ubiquitination. Part of Cul5-RING ubiquitin ligase complex. Is active in nucleus.

Source: NCBI Gene 90864 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 2 total
  • MANE Select transcript: NM_080861

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30629
Approved symbolSPSB3
NamesplA/ryanodine receptor domain and SOCS box containing 3
Location16p13.3
Locus typegene with protein product
StatusApproved
AliasesSSB-3
Ensembl geneENSG00000162032
Ensembl biotypeprotein_coding
OMIM611659
Entrez90864

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 19 protein_coding, 9 retained_intron

ENST00000301717, ENST00000563668, ENST00000563705, ENST00000563741, ENST00000564070, ENST00000564709, ENST00000565550, ENST00000566339, ENST00000567868, ENST00000568416, ENST00000569380, ENST00000569769, ENST00000890579, ENST00000890580, ENST00000890581, ENST00000890582, ENST00000890583, ENST00000890584, ENST00000890585, ENST00000890586, ENST00000890587, ENST00000890588, ENST00000890589, ENST00000890590, ENST00000965197, ENST00000965198, ENST00000965199, ENST00000965200

RefSeq mRNA: 2 — MANE Select: NM_080861 NM_001324081, NM_080861

CCDS: CCDS32365

Canonical transcript exons

ENST00000566339 — 7 exons

ExonStartEnd
ENSE0000262125817825021782571
ENSE0000262309517767121777443
ENSE0000347165917813581781495
ENSE0000349293417781341778321
ENSE0000354199417777471777872
ENSE0000358945517784351778612
ENSE0000364361917779461778048

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 99.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.1462 / max 84.1634, expressed in 1782 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
15586910.99291782
1558700.306824
1558680.153353

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pancreatic ductal cellCL:000207999.40gold quality
right hemisphere of cerebellumUBERON:001489097.58gold quality
cerebellar hemisphereUBERON:000224597.52gold quality
cerebellar cortexUBERON:000212997.44gold quality
granulocyteCL:000009497.41gold quality
lower esophagus mucosaUBERON:003583497.41gold quality
upper leg skinUBERON:000426297.22gold quality
cerebellumUBERON:000203797.00gold quality
skin of hipUBERON:000155496.89gold quality
skin of legUBERON:000151196.71gold quality
mucosa of stomachUBERON:000119996.67gold quality
endothelial cellCL:000011596.61gold quality
right lobe of liverUBERON:000111496.56gold quality
skin of abdomenUBERON:000141696.53gold quality
apex of heartUBERON:000209896.36gold quality
left ovaryUBERON:000211996.29gold quality
gastrocnemiusUBERON:000138896.24gold quality
left adrenal gland cortexUBERON:003582596.24gold quality
cervix squamous epitheliumUBERON:000692296.10gold quality
adrenal cortexUBERON:000123596.03gold quality
left adrenal glandUBERON:000123495.99gold quality
hindlimb stylopod muscleUBERON:000425295.94gold quality
right ovaryUBERON:000211895.92gold quality
right adrenal glandUBERON:000123395.90gold quality
right adrenal gland cortexUBERON:003582795.87gold quality
body of pancreasUBERON:000115095.84gold quality
amniotic fluidUBERON:000017395.69gold quality
body of stomachUBERON:000116195.63gold quality
zone of skinUBERON:000001495.59gold quality
esophagogastric junction muscularis propriaUBERON:003584195.57gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.34
E-MTAB-4850no585.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting SPSB3, 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-4533100.0069.482758
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-7845-5P99.8864.88771
HSA-MIR-391999.8769.452489
HSA-MIR-548AU-3P99.7068.221373
HSA-MIR-472999.6972.184233
HSA-MIR-320299.6667.702737
HSA-MIR-584-3P99.3567.691082
HSA-MIR-751599.3168.221795
HSA-MIR-3678-3P99.3167.101432
HSA-MIR-315498.9466.551455
HSA-MIR-6501-3P98.7167.451480
HSA-MIR-2467-3P98.6567.181969
HSA-MIR-6842-3P98.0766.331325
HSA-MIR-1910-5P97.4266.36844
HSA-MIR-447597.3666.95761
HSA-MIR-4690-3P97.0264.72981
HSA-MIR-568597.0264.341004
HSA-MIR-125896.0867.74700
HSA-MIR-394395.8764.57523

Literature-anchored findings (GeneRIF, showing 2)

  • Low SPSB3 expression is associated with lymph node metastasis in Ovarian and esophageal squamous cell carcinoma. (PMID:29059170)
  • The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation. (PMID:38418882)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriospsb3aENSDARG00000077737
mus_musculusSpsb3ENSMUSG00000024160
rattus_norvegicusSpsb3ENSRNOG00000015300
drosophila_melanogasterCG10516FBGN0036549

Paralogs (4): SPSB2 (ENSG00000111671), SPSB1 (ENSG00000171621), FBXO45 (ENSG00000174013), SPSB4 (ENSG00000175093)

Protein

Protein identifiers

SPRY domain-containing SOCS box protein 3Q6PJ21 (reviewed: Q6PJ21)

All UniProt accessions (2): Q6PJ21, H3BP12

UniProt curated annotations — full annotation on UniProt →

Function. Substrate-recognition component of a cullin-5-RING E3 ubiquitin-protein ligase complex (ECS complex, also named CRL5 complex), which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as CGAS and SNAI1. The ECS(SPSB3) complex catalyzes ‘Lys-48’-linked ubiquitination of nuclear CGAS in cycling cells, leading to its degradation. Recognizes and binds nucleosome-bound CGAS: ubiquitination and degradation of nuclear CGAS during G1 and G2 phases is required to promote low intranuclear CGAS abundance before the next mitotic cycle. The ECS(SPSB3) complex also mediates ubiquitination and degradation of phosphorylated SNAI1.

Subunit / interactions. Substrate-recognition component of the ECS(SPSB3) complex, composed of SPSB3, CUL5, ELOB, ELOC and RNF7/RBX2. Interacts with MET.

Subcellular location. Nucleus.

Domain organisation. The SOCS box domain mediates the interaction with the Elongin BC complex, an adapter module in different E3 ubiquitin ligase complexes.

Pathway. Protein modification; protein ubiquitination.

Similarity. Belongs to the SPSB family.

RefSeq proteins (2): NP_001311010, NP_543137* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001496SOCS_boxDomain
IPR001870B30.2/SPRYDomain
IPR003877SPRY_domDomain
IPR013320ConA-like_dom_sfHomologous_superfamily
IPR035754SPRY_SPSB3Domain
IPR043136B30.2/SPRY_sfHomologous_superfamily
IPR050672FBXO45-Fsn/SPSB_familiesFamily

Pfam: PF00622

UniProt features (34 total): strand 15, turn 5, sequence conflict 4, domain 2, region of interest 2, helix 2, mutagenesis site 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
8OL1ELECTRON MICROSCOPY3.5
8OKXELECTRON MICROSCOPY3.51

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6PJ21-F177.010.63

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 (2):

PositionPhenotype
160–162abolished interaction with cgas; when associated with 259-a–a-262.
259–262abolished interaction with cgas; when associated with 160-a–a-162.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-8951664Neddylation
R-HSA-392499Metabolism of proteins
R-HSA-597592Post-translational protein modification

MSigDB gene sets: 170 (showing top): STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_MESENCHYMAL_CELL_DIFFERENTIATION, BLALOCK_ALZHEIMERS_DISEASE_UP, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_PROTEIN_POLYUBIQUITINATION, STONER_ESOPHAGEAL_CARCINOGENESIS_UP

GO Biological Process (8): negative regulation of epithelial to mesenchymal transition (GO:0010719), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), protein K48-linked ubiquitination (GO:0070936), negative regulation of cGAS/STING signaling pathway (GO:0160049), epithelial to mesenchymal transition (GO:0001837), ubiquitin-dependent protein catabolic process (GO:0006511), protein ubiquitination (GO:0016567), cGAS/STING signaling pathway (GO:0140896)

GO Molecular Function (2): ubiquitin-like ligase-substrate adaptor activity (GO:1990756), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), cytosol (GO:0005829), SCF ubiquitin ligase complex (GO:0019005), Cul5-RING ubiquitin ligase complex (GO:0031466)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Post-translational protein modification1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cullin-RING ubiquitin ligase complex2
epithelial to mesenchymal transition1
regulation of epithelial to mesenchymal transition1
negative regulation of cell differentiation1
negative regulation of multicellular organismal process1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
protein polyubiquitination1
negative regulation of cytoplasmic pattern recognition receptor signaling pathway1
cGAS/STING signaling pathway1
mesenchymal cell differentiation1
protein ubiquitination1
modification-dependent protein catabolic process1
protein modification by small protein conjugation1
cytoplasmic pattern recognition receptor signaling pathway1
enzyme-substrate adaptor activity1
binding1
intracellular membrane-bounded organelle1
cytoplasm1
cellular anatomical structure1

Protein interactions and networks

STRING

720 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SPSB3CISHQ9NSE2763
SPSB3SPSB1Q96BD6494
SPSB3FBXL14Q8N1E6490
SPSB3SPSB2Q99619478
SPSB3KLHL38Q2WGJ6450
SPSB3ANKRD29Q8N6D5444
SPSB3TRIM21P19474422
SPSB3SPSB4Q96A44422
SPSB3OR4A5Q8NH83419
SPSB3BTNL3Q6UXE8418
SPSB3BTNL8Q6UX41416
SPSB3BTN2A1P78408411
SPSB3FBXO11Q86XK2410
SPSB3FBXL5Q9UKA1398
SPSB3OR4C12Q96R67396

IntAct

67 interactions, top by confidence:

ABTypeScore
PGBD1ZNF24psi-mi:“MI:0914”(association)0.900
CUL5SOCS2psi-mi:“MI:0914”(association)0.880
CDK13CCNKpsi-mi:“MI:0914”(association)0.830
SMYD1ADSS2psi-mi:“MI:0914”(association)0.780
SPSB3ENKD1psi-mi:“MI:0915”(physical association)0.720
ENKD1SPSB3psi-mi:“MI:0915”(physical association)0.720
CUL5SOCS7psi-mi:“MI:0914”(association)0.640
NUMBSLC1A1psi-mi:“MI:0914”(association)0.640
GNPTGGNPTABpsi-mi:“MI:0914”(association)0.620
SPSB3psi-mi:“MI:0915”(physical association)0.560
SPSB3psi-mi:“MI:0915”(physical association)0.560
SPSB3NUMBLpsi-mi:“MI:0915”(physical association)0.560
SPSB3ZNF396psi-mi:“MI:0915”(physical association)0.560
GRNSPSB3psi-mi:“MI:0915”(physical association)0.560
RPGRNPHP1psi-mi:“MI:0914”(association)0.560
GPN3POLR3Apsi-mi:“MI:0914”(association)0.530
POLR1CPOLR3Apsi-mi:“MI:0914”(association)0.530
RNF7SOCS7psi-mi:“MI:0914”(association)0.530
HSP90AB1SPSB3psi-mi:“MI:0915”(physical association)0.400
MAPK8IP2SPSB3psi-mi:“MI:0915”(physical association)0.370
CSNK2BSPSB3psi-mi:“MI:0915”(physical association)0.370
SPSB3CFTRpsi-mi:“MI:0915”(physical association)0.370
CUL5DDX3Xpsi-mi:“MI:0914”(association)0.350

BioGRID (57): SPSB3 (Two-hybrid), SPSB3 (Two-hybrid), SPSB3 (Affinity Capture-RNA), SPSB3 (Affinity Capture-MS), SPSB3 (Affinity Capture-MS), SPSB3 (Two-hybrid), SPSB3 (Affinity Capture-MS), SPSB3 (Affinity Capture-MS), SPSB3 (Affinity Capture-MS), SPSB3 (Affinity Capture-MS), SPSB3 (Affinity Capture-MS), SPSB3 (Affinity Capture-MS), SPSB3 (Affinity Capture-MS), SPSB3 (Affinity Capture-MS), SPSB3 (Affinity Capture-MS)

ESM2 similar proteins: A1L0Y2, A2ALK8, A2ARP1, A2Z8S0, A4IFG2, A8XT88, B1AVZ0, B3M1E1, B3P4N5, B4GZ20, B4HJC0, B4KA23, B4LVS8, B4NKI9, B4PVH6, B4QVW6, M9MRI4, O35242, O76050, P0C644, P26045, Q18223, Q29B63, Q29RQ5, Q3MHZ2, Q3UJK4, Q571F5, Q5M870, Q5NCX5, Q5PQR3, Q5R881, Q6PFW1, Q6PJ21, Q75G68, Q8BVR6, Q8C726, Q8CJC5, Q8R516, Q91YL3, Q91ZY8

Diamond homologs: A1Z6E0, A8QGZ7, A8XT88, B0X9V1, B3MDR0, B3NRP1, B4F739, B4GBN7, B4HQ29, B4J6Q0, B4KNC5, B4LMQ3, B4MR59, B4P4K8, B4QE02, O88838, P0C2W1, P0CH38, Q16XV7, Q18223, Q290L5, Q3MHZ2, Q571F5, Q5E9X6, Q5M877, Q6NZ03, Q6PJ21, Q7QGL9, Q7ZXY1, Q8K3B1, Q8R5B6, Q96A44, Q96BD6, Q99619, Q9D5L7, Q9V6L9, Q28DT9, Q5M9B1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 56 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
Neutrophil degranulation95.5×3e-03

GO biological processes:

GO termPartnersFoldFDR
positive regulation of cell migration77.9×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2635 predictions. Top by Δscore:

VariantEffectΔscore
16:1777441:CAC:Cacceptor_gain1.0000
16:1777442:ACCT:Aacceptor_loss1.0000
16:1777444:CTGGA:Cacceptor_loss1.0000
16:1777741:CCTCA:Cdonor_loss1.0000
16:1777742:CTCA:Cdonor_loss1.0000
16:1777743:TCAC:Tdonor_loss1.0000
16:1777745:ACCT:Adonor_loss1.0000
16:1777746:C:Tdonor_loss1.0000
16:1777756:T:TAdonor_gain1.0000
16:1777757:C:Adonor_gain1.0000
16:1777873:C:CCacceptor_gain1.0000
16:1778129:CTTA:Cdonor_loss1.0000
16:1778130:TTACC:Tdonor_loss1.0000
16:1778131:TAC:Tdonor_loss1.0000
16:1778132:A:ACdonor_gain1.0000
16:1778132:AC:Adonor_gain1.0000
16:1778133:C:CAdonor_gain1.0000
16:1778133:CC:Cdonor_gain1.0000
16:1778133:CCA:Cdonor_gain1.0000
16:1778133:CCAT:Cdonor_gain1.0000
16:1778133:CCATG:Cdonor_gain1.0000
16:1778319:AATCT:Aacceptor_loss1.0000
16:1778320:ATCT:Aacceptor_loss1.0000
16:1778321:TCT:Tacceptor_loss1.0000
16:1778322:C:CAacceptor_loss1.0000
16:1778322:C:CCacceptor_gain1.0000
16:1778323:T:Gacceptor_loss1.0000
16:1778428:CG:Cdonor_gain1.0000
16:1778433:A:ACdonor_gain1.0000
16:1778434:C:CCdonor_gain1.0000

AlphaMissense

2332 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:1777995:G:CF182L1.000
16:1777995:G:TF182L1.000
16:1777997:A:GF182L1.000
16:1778144:C:TG161D1.000
16:1778175:A:GW151R1.000
16:1778175:A:TW151R1.000
16:1778307:A:GW107R1.000
16:1778307:A:TW107R1.000
16:1777376:G:CS263R0.999
16:1777376:G:TS263R0.999
16:1777378:T:GS263R0.999
16:1777383:G:TA261D0.999
16:1777392:G:AS258F0.999
16:1777392:G:TS258Y0.999
16:1777393:A:GS258P0.999
16:1777394:G:CC257W0.999
16:1777396:A:GC257R0.999
16:1777776:A:GL231P0.999
16:1777797:A:GL224P0.999
16:1777809:A:TI220N0.999
16:1777826:G:CF214L0.999
16:1777826:G:TF214L0.999
16:1777828:A:GF214L0.999
16:1777872:C:AG199V0.999
16:1777872:C:TG199D0.999
16:1777952:A:CY197D0.999
16:1777954:G:AS196F0.999
16:1777955:A:GS196P0.999
16:1777957:A:GL195P0.999
16:1777960:C:TG194D0.999

dbSNP variants (sampled 300 via entrez): RS1000513546 (16:1776370 CAG>C), RS1000560342 (16:1778867 A>G), RS1000967235 (16:1779124 C>T), RS1001138988 (16:1784052 C>A,T), RS1001221004 (16:1780501 G>A), RS1001626436 (16:1780661 G>A), RS1001868867 (16:1783851 G>A,T), RS1002250848 (16:1783589 A>C), RS1002479993 (16:1783220 C>G,T), RS1003003991 (16:1781528 G>T), RS1003051504 (16:1781757 C>T), RS1003647232 (16:1782601 G>A), RS1003856156 (16:1779708 G>A,C), RS1004116517 (16:1779572 G>A,C), RS1004344436 (16:1776594 C>T)

Disease associations

OMIM: gene MIM:611659 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST010320_29PR interval3.000000e-09
GCST010321_49PR interval1.000000e-09
GCST90000025_76Appendicular lean mass2.000000e-23
GCST90000026_8Appendicular lean mass5.000000e-14
GCST90000027_33Appendicular lean mass4.000000e-11
GCST90002400_167Plateletcrit2.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004462PR interval
EFO:0004980appendicular lean mass
EFO:0007985platelet crit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, increases expression2
sodium arseniteaffects cotreatment, decreases expression, increases abundance, increases expression2
Arsenicaffects methylation, affects cotreatment, decreases expression, increases abundance2
Tunicamycinincreases expression2
Valproic Acidincreases methylation, affects expression2
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
trichostatin Aaffects expression1
beta-lapachoneincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
cobaltous chlorideincreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
perfluorooctane sulfonic acidincreases expression1
K 7174increases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
ICG 001increases expression1
licochalcone Bincreases expression1
jinfukangaffects cotreatment, increases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Bortezomibincreases expression1
Resveratroldecreases expression1
Temozolomideincreases expression1
Acroleinincreases abundance, affects cotreatment, increases oxidation1
Air Pollutantsincreases abundance, increases oxidation, affects cotreatment1
Cisplatinincreases expression, affects cotreatment1
Diurondecreases expression1
Estradioldecreases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases 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.