SYNJ2BP

gene
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Also known as Arip2

Summary

SYNJ2BP (synaptojanin 2 binding protein, HGNC:18955) is a protein-coding gene on chromosome 14q24.2, encoding Synaptojanin-2-binding protein (P57105). Regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction.

Predicted to enable type II activin receptor binding activity. Involved in several processes, including negative regulation of endothelial cell migration; negative regulation of sprouting angiogenesis; and regulation of signal transduction. Located in mitochondrial outer membrane.

Source: NCBI Gene 55333 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 4 total
  • MANE Select transcript: NM_018373

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18955
Approved symbolSYNJ2BP
Namesynaptojanin 2 binding protein
Location14q24.2
Locus typegene with protein product
StatusApproved
AliasesArip2
Ensembl geneENSG00000213463
Ensembl biotypeprotein_coding
OMIM609411
Entrez55333

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000256366, ENST00000554216, ENST00000863002, ENST00000863003, ENST00000863004, ENST00000863005, ENST00000936942

RefSeq mRNA: 1 — MANE Select: NM_018373 NM_018373

CCDS: CCDS9803

Canonical transcript exons

ENST00000256366 — 4 exons

ExonStartEnd
ENSE000006588517038847070388606
ENSE000008078647036649970373131
ENSE000025332027041690070417090
ENSE000035846287037567670375771

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 96.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.3357 / max 188.6881, expressed in 1723 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
14391620.33571723

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
renal medullaUBERON:000036296.94gold quality
cardia of stomachUBERON:000116296.77gold quality
body of tongueUBERON:001187695.49gold quality
pylorusUBERON:000116695.24gold quality
saphenous veinUBERON:000731895.07gold quality
biceps brachiiUBERON:000150794.81gold quality
jejunumUBERON:000211594.79gold quality
vena cavaUBERON:000408794.78gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450294.61gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451194.52gold quality
urethraUBERON:000005794.47gold quality
oocyteCL:000002394.05gold quality
jejunal mucosaUBERON:000039993.76gold quality
trigeminal ganglionUBERON:000167593.67gold quality
heart right ventricleUBERON:000208093.51gold quality
superior surface of tongueUBERON:000737192.55gold quality
epithelium of nasopharynxUBERON:000195192.43gold quality
nasopharynxUBERON:000172892.41gold quality
dorsal root ganglionUBERON:000004492.23gold quality
vastus lateralisUBERON:000137992.16gold quality
mucosa of sigmoid colonUBERON:000499392.08gold quality
tongueUBERON:000172392.02gold quality
seminal vesicleUBERON:000099891.88gold quality
pericardiumUBERON:000240791.86gold quality
duodenumUBERON:000211491.76gold quality
left ventricle myocardiumUBERON:000656691.60gold quality
subthalamic nucleusUBERON:000190691.56gold quality
myocardiumUBERON:000234991.52gold quality
cauda epididymisUBERON:000436091.38gold quality
visceral pleuraUBERON:000240191.24gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes12.26
E-GEOD-111727no1165.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

252 targeting SYNJ2BP, 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-6873-3P100.0071.422626
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-3163100.0077.238605
HSA-MIR-3646100.0073.565283
HSA-MIR-9-5P100.0072.282361
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-340-5P100.0072.504437
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-511-3P99.9968.851467
HSA-MIR-366299.9973.825684
HSA-MIR-150-5P99.9966.691976
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-453499.9966.581907
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-548P99.9872.253784
HSA-MIR-1213699.9872.815713
HSA-MIR-548N99.9871.944170
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-806899.9873.852376
HSA-MIR-480399.9871.993117
HSA-MIR-548AN99.9770.912817
HSA-MIR-1229-3P99.9766.49906
HSA-MIR-512-3P99.9767.351049

Literature-anchored findings (GeneRIF, showing 8)

  • These results suggest that ARIP2 is a putative growth-promoting factor involved in breast tumorigenesis and tumor development. (PMID:19349195)
  • Synaptojanin-2 binding protein stabilizes the Notch ligands DLL1 and DLL4 and inhibits sprouting angiogenesis. (PMID:24025447)
  • Ubiquilins are a family of chaperones for cytosolically exposed transmembrane domains and use ubiquitin to triage clients, like Omp25, for degradation via coordinated intra- and intermolecular interactions. (PMID:27345149)
  • Data found that SYNJ2BP was decreased in hepatocellular carcinoma (HCC) tissues and cell lines and provide evidence that SYNJ2BP may act as a tumor suppressor during HCC development activating DLL4 pathway. (PMID:27440153)
  • The increased ARIP2 in the LPS-activated macrophages may play an anti-inflammatory role via inhibiting the production of pro-inflammatory cytokines by feedback regulation, which is related to the inhibition of CD14 expression on macrophages. (PMID:28871189)
  • The mitochondrial outer membrane protein SYNJ2BP interacts with the cell adhesion molecule TMIGD1 and can recruit it to mitochondria. (PMID:32303178)
  • The PDZ Domain Protein SYNJ2BP Regulates GRK-Dependent Sst2A Phosphorylation and Downstream MAPK Signaling. (PMID:33313679)
  • SYNJ2BP ameliorates intervertebral disc degeneration by facilitating mitochondria-associated endoplasmic reticulum membrane formation and mitochondrial Zn[2+] homeostasis. (PMID:38158052)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriosynj2bpENSDARG00000028321
mus_musculusSynj2bpENSMUSG00000090935
rattus_norvegicusSynj2bpENSRNOG00000006399

Paralogs (2): COX16 (ENSG00000133983), KIAA1614 (ENSG00000135835)

Protein

Protein identifiers

Synaptojanin-2-binding proteinP57105 (reviewed: P57105)

Alternative names: Mitochondrial outer membrane protein 25

All UniProt accessions (1): P57105

UniProt curated annotations — full annotation on UniProt →

Function. Regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction.

Subunit / interactions. Binds (via the PDZ domain) to isoform 2A of SYNJ2 (via the unique motif in the C-terminus). Interacts (via C-terminus) with RALBP1. Interacts (via PDZ domain) with ACVR2A (via C-terminus) and ACVR2B (via C-terminus). Forms a ternary complex with ACVR2A and RALBP1. Interacts with MAPK12. Interacts with DLL1; enhances DLL1 protein stability, and promotes notch signaling in endothelial cells.

Subcellular location. Mitochondrion outer membrane.

RefSeq proteins (1): NP_060843* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001478PDZDomain
IPR036034PDZ_sfHomologous_superfamily
IPR050614Synaptic_Scaffolding_LAP-MAGUKFamily

Pfam: PF00595

UniProt features (19 total): strand 8, helix 3, topological domain 2, chain 1, turn 1, transmembrane region 1, domain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

9 structures.

PDBMethodResolution (Å)
2JIKX-RAY DIFFRACTION1.35
2JINX-RAY DIFFRACTION1.5
7P73X-RAY DIFFRACTION1.85
7P74X-RAY DIFFRACTION1.9
8AELX-RAY DIFFRACTION2.2
7PC9X-RAY DIFFRACTION2.4
7R2MX-RAY DIFFRACTION2.4
7R2TX-RAY DIFFRACTION2.5
2ENOSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P57105-F178.600.54

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 194 (showing top): GOBP_NEGATIVE_REGULATION_OF_EPITHELIAL_CELL_PROLIFERATION, GOBP_NEGATIVE_REGULATION_OF_ERK1_AND_ERK2_CASCADE, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GOBP_PROTEIN_TARGETING, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_NEGATIVE_REGULATION_OF_MAPK_CASCADE, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_SPROUTING_ANGIOGENESIS, chr14q24, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_NEGATIVE_REGULATION_OF_SPROUTING_ANGIOGENESIS, GOBP_REGULATION_OF_ENDOTHELIAL_CELL_MIGRATION

GO Biological Process (9): negative regulation of endothelial cell proliferation (GO:0001937), protein targeting (GO:0006605), Rho protein signal transduction (GO:0007266), regulation of Notch signaling pathway (GO:0008593), negative regulation of endothelial cell migration (GO:0010596), negative regulation of angiogenesis (GO:0016525), regulation of endocytosis (GO:0030100), negative regulation of ERK1 and ERK2 cascade (GO:0070373), negative regulation of sprouting angiogenesis (GO:1903671)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
endothelial cell proliferation1
regulation of endothelial cell proliferation1
negative regulation of epithelial cell proliferation1
establishment of protein localization1
small GTPase-mediated signal transduction1
Notch signaling pathway1
regulation of signal transduction1
regulation of endothelial cell migration1
negative regulation of cell migration1
endothelial cell migration1
angiogenesis1
regulation of angiogenesis1
negative regulation of blood vessel morphogenesis1
endocytosis1
regulation of cellular component organization1
regulation of vesicle-mediated transport1
negative regulation of MAPK cascade1
ERK1 and ERK2 cascade1
regulation of ERK1 and ERK2 cascade1
sprouting angiogenesis1
negative regulation of angiogenesis1
regulation of sprouting angiogenesis1
binding1
cytoplasm1
intracellular membrane-bounded organelle1
mitochondrial membrane1
organelle outer membrane1
cellular anatomical structure1

Protein interactions and networks

STRING

1076 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SYNJ2BPA0A087WVV2A0A087WVV2987
SYNJ2BPSYNJ2O15056892
SYNJ2BPABITRAMQ9NX38826
SYNJ2BPRALAP11233776
SYNJ2BPPEX26Q7Z412700
SYNJ2BPSLAMF1Q13291672
SYNJ2BPAMPHP49418669
SYNJ2BPPEX6Q13608668
SYNJ2BPSYNJ1O43426667
SYNJ2BPACVR2AP27037656
SYNJ2BPTMIGD1Q6UXZ0623
SYNJ2BPBIN1O00499549
SYNJ2BPTOMM20Q15388505
SYNJ2BPSH3GL2Q99962505
SYNJ2BPBCAP31P51572496

IntAct

545 interactions, top by confidence:

ABTypeScore
ESYT1ESYT2psi-mi:“MI:0914”(association)0.770
SYNJ2BPUSHBP1psi-mi:“MI:0915”(physical association)0.720
USHBP1SYNJ2BPpsi-mi:“MI:0915”(physical association)0.720
SYNJ2BPAQP6psi-mi:“MI:0915”(physical association)0.680
E6SYNJ2BPpsi-mi:“MI:0407”(direct interaction)0.640
TaxSYNJ2BPpsi-mi:“MI:0407”(direct interaction)0.640
SYNJ2BPTaxpsi-mi:“MI:0915”(physical association)0.640
SYNJ2BPE6psi-mi:“MI:0915”(physical association)0.640
SYNJ2BPDLL1psi-mi:“MI:0915”(physical association)0.610
SYNJ2BPRPS6KA1psi-mi:“MI:0407”(direct interaction)0.610
E6SYNJ2BPpsi-mi:“MI:0407”(direct interaction)0.610
SYNJ2BPE6psi-mi:“MI:0915”(physical association)0.610
RPS6KA1SYNJ2BPpsi-mi:“MI:0915”(physical association)0.610
NET1SYNJ2BPpsi-mi:“MI:0407”(direct interaction)0.610
SLC16A3CASKpsi-mi:“MI:0914”(association)0.590
KARS1SYNJ2BPpsi-mi:“MI:0407”(direct interaction)0.590
RRBP1SYNJ2BPpsi-mi:“MI:0407”(direct interaction)0.590
VANGL1SYNJ2BPpsi-mi:“MI:0407”(direct interaction)0.590
SYNJ2BPDLL4psi-mi:“MI:0915”(physical association)0.560

BioGRID (167): USHBP1 (Two-hybrid), SYNJ2BP (Affinity Capture-MS), SYNJ2BP (Affinity Capture-MS), SYNJ2BP (Affinity Capture-MS), SYNJ2BP (Affinity Capture-MS), SYNJ2BP (Two-hybrid), BAG6 (Reconstituted Complex), UBQLN1 (Reconstituted Complex), UBQLN4 (Reconstituted Complex), ASNA1 (Reconstituted Complex), UBL4A (Reconstituted Complex), UBQLN2 (Reconstituted Complex), UBQLN1 (Reconstituted Complex), SYNJ2BP (Affinity Capture-MS), SYNJ2BP (Protein-peptide)

ESM2 similar proteins: A0A8C0TYJ0, A0A8I5ZNK2, A6QQZ7, A8KBF6, B2RYD2, O00560, O88506, O95747, P19517, P31016, P57105, P70175, P78352, Q12959, Q15139, Q15700, Q28C55, Q3T0C9, Q3US41, Q5PYH5, Q5PYH6, Q5PYH7, Q5R495, Q5T2T1, Q5U2Y3, Q62108, Q62696, Q62936, Q63622, Q640Z1, Q6DEZ7, Q6DJD3, Q6NXB2, Q6NXG1, Q6P0D7, Q6P9R2, Q6R005, Q7ZY29, Q811D0, Q863I2

Diamond homologs: A0A0G2K2P5, A0A8P0N4K0, C5IAW9, F1LW30, O08721, O08722, O08747, O62683, O95049, O95185, O97758, P39447, P57105, Q07157, Q0P5E6, Q13424, Q28626, Q32LE7, Q3T0C9, Q5EBL8, Q5ZIK2, Q61234, Q6NXB2, Q6QA76, Q6R653, Q6UXZ4, Q6ZN44, Q761X5, Q7KRY7, Q7T2Z5, Q80VW5, Q86UL8, Q8IV45, Q8IZJ1, Q8JGT4, Q8K1S2, Q8K1S3, Q8K1S4, Q95168, Q9CZG9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 139 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
SLC-mediated transmembrane transport106.7×6e-04
Transport of small molecules164.5×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance4
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

737 predictions. Top by Δscore:

VariantEffectΔscore
14:70375670:ACCT:Adonor_loss1.0000
14:70375671:CCTA:Cdonor_loss1.0000
14:70375672:CTA:Cdonor_loss1.0000
14:70375673:TA:Tdonor_loss1.0000
14:70375674:AC:Adonor_gain1.0000
14:70375674:ACCCT:Adonor_loss1.0000
14:70375675:C:CGdonor_loss1.0000
14:70375675:CC:Cdonor_gain1.0000
14:70375767:TTTAC:Tacceptor_gain1.0000
14:70375768:TTAC:Tacceptor_gain1.0000
14:70375769:TAC:Tacceptor_gain1.0000
14:70375772:C:CCacceptor_gain1.0000
14:70375772:C:Gacceptor_loss1.0000
14:70388482:A:ACdonor_gain1.0000
14:70388482:ATCAC:Adonor_gain1.0000
14:70388489:T:Adonor_gain1.0000
14:70388489:T:TAdonor_gain1.0000
14:70388617:CA:Cacceptor_gain1.0000
14:70416896:ATAC:Adonor_loss1.0000
14:70416897:TACCT:Tdonor_loss1.0000
14:70416898:ACC:Adonor_loss1.0000
14:70416898:ACCT:Adonor_loss1.0000
14:70416899:C:CAdonor_loss1.0000
14:70416929:T:TAdonor_gain1.0000
14:70375674:A:ACdonor_gain0.9900
14:70375674:ACC:Adonor_gain0.9900
14:70375675:C:CCdonor_gain0.9900
14:70375675:CCC:Cdonor_gain0.9900
14:70375675:CCCT:Cdonor_gain0.9900
14:70375705:AG:Adonor_gain0.9900

AlphaMissense

942 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:70388477:A:GI65T1.000
14:70388540:A:TV44D1.000
14:70388591:A:TI27N1.000
14:70388597:A:GF25S1.000
14:70375692:A:GL94P0.999
14:70375719:A:GF85S0.999
14:70388472:A:GS67P0.999
14:70388477:A:CI65S0.999
14:70388495:A:GL59P0.999
14:70388495:A:TL59H0.999
14:70388591:A:CI27S0.999
14:70388600:C:AG24V0.999
14:70388601:C:GG24R0.999
14:70416917:A:GL16P0.999
14:70375741:G:CH78D0.998
14:70388477:A:TI65N0.998
14:70388483:T:AD63V0.998
14:70388483:T:CD63G0.998
14:70388498:C:GR58P0.998
14:70388582:C:TG30E0.998
14:70388585:C:AG29V0.998
14:70388585:C:TG29D0.998
14:70388586:C:AG29C0.998
14:70388586:C:GG29R0.998
14:70388591:A:GI27T0.998
14:70388600:C:TG24D0.998
14:70388601:C:AG24C0.998
14:70375722:A:GL84P0.997
14:70375732:C:GA81P0.997
14:70375767:T:AN69I0.997

dbSNP variants (sampled 300 via entrez): RS1000003707 (14:70387388 G>C,T), RS1000014228 (14:70404744 G>A), RS1000258763 (14:70400199 A>G), RS1000276119 (14:70380504 A>T), RS1000285168 (14:70392523 A>G), RS1000518135 (14:70414299 C>A), RS1000628183 (14:70368544 T>C), RS1000734824 (14:70375274 T>C), RS1000746111 (14:70379203 T>C), RS1000868192 (14:70417035 G>A,T), RS1000922813 (14:70386048 T>C), RS1000979830 (14:70371437 G>A), RS1001000250 (14:70388862 TAAAG>T), RS1001141443 (14:70410082 T>C), RS1001156147 (14:70395724 A>G)

Disease associations

OMIM: gene MIM:609411 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST002497_28Blood pressure6.000000e-07
GCST006612_94LDL cholesterol3.000000e-11
GCST007448_12Normal facial asymmetry (angle of surface orientation score)2.000000e-08
GCST010396_4Gut microbiota (bacterial taxa, hurdle binary method)9.000000e-06
GCST012137_4Motor coordination2.000000e-06

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0006335systolic blood pressure
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0009751facial asymmetry measurement
EFO:0007874gut microbiome measurement
EFO:0010749motor function measurement

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
Cyclosporinedecreases expression2
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, increases methylation1
perfluorooctanoic acidincreases expression1
4-aminophenylarsenoxideaffects binding, decreases reaction1
CGP 52608affects binding, increases reaction1
abrinedecreases 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
Temozolomidedecreases expression1
Arsenic Trioxideaffects binding, decreases reaction1
Fulvestrantaffects cotreatment, increases methylation1
Acetaminophendecreases expression1
Air Pollutantsincreases expression, increases abundance1
Atrazinedecreases expression1
Coumestroldecreases expression1
Ethyl Methanesulfonateincreases expression1
Smokeincreases abundance, increases expression1
Thimerosaldecreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Tunicamycindecreases expression1
Valproic Acidaffects expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases 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.