Gene Gene information from NCBI Gene database.
Entrez ID 8867
Gene name Synaptojanin 1
Gene symbol SYNJ1
Synonyms (NCBI Gene)
DEE53EIEE53INPP5GPARK20
Chromosome 21
Chromosome location 21q22.11
Summary This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. Multiple transcript variants encoding d
SNPs SNP information provided by dbSNP.
13
SNP ID Visualize variation Clinical significance Consequence
rs145937537 G>A Conflicting-interpretations-of-pathogenicity Missense variant, coding sequence variant
rs398122403 C>T Pathogenic Missense variant, coding sequence variant
rs778394516 CTTAT>- Pathogenic Frameshift variant, coding sequence variant
rs886039732 TTTGT>- Pathogenic Frameshift variant, coding sequence variant
rs1057524877 T>C Pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
266
miRTarBase ID miRNA Experiments Reference
MIRT027224 hsa-miR-103a-3p Sequencing 20371350
MIRT028365 hsa-miR-32-5p Sequencing 20371350
MIRT031926 hsa-miR-16-5p Sequencing 20371350
MIRT049591 hsa-miR-92a-3p CLASH 23622248
MIRT047739 hsa-miR-10a-5p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
56
GO ID Ontology Definition Evidence Reference
GO:0003676 Function Nucleic acid binding IEA
GO:0003723 Function RNA binding IEA
GO:0004438 Function Phosphatidylinositol-3-phosphate phosphatase activity IDA 18093523
GO:0004438 Function Phosphatidylinositol-3-phosphate phosphatase activity TAS
GO:0004439 Function Phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
604297 11503 ENSG00000159082
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O43426
Protein name Synaptojanin-1 (EC 3.1.3.36) (Synaptic inositol 1,4,5-trisphosphate 5-phosphatase 1)
Protein function Phosphatase that acts on various phosphoinositides, including phosphatidylinositol 4-phosphate, phosphatidylinositol (4,5)-bisphosphate and phosphatidylinositol (3,4,5)-trisphosphate (PubMed:23804563, PubMed:27435091). Has a role in clathrin-med
PDB 1W80 , 2DNR , 2VJ0 , 7A0V
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02383 Syja_N 60 340 SacI homology domain Family
PF03372 Exo_endo_phos 538 859 Endonuclease/Exonuclease/phosphatase family Domain
PF08952 DUF1866 867 1009 Domain of unknown function (DUF1866) Domain
Sequence
MAFSKGFRIYHKLDPPPFSLIVETRHKEECLMFESGAVAVLSSAEKEAIKGTYSKVLDAY
GLLGVLRLNLGDTMLHYLVLVTGCMSVGKIQESEVFRVTSTEFISLRIDSSDEDRISEVR
KVLNSGNFYFAWSASGISLDLSLNAHRSMQEQTTDNRFFWNQSLHLHLKHYGVNCDDWLL
RLMCGGVEIRTIYAAHKQAKACLISRLSCERAGTRFNVRGTNDDGHVANFVETEQVVYLD
DSVSSFIQIRGSVPLFWEQPGLQVGSHRVRMSRGFEANAPAFDRHFRTLKNLYGKQIIVN
LLGSKEGEHMLSKAFQSHLKASEHAADIQMVNFDYHQMVK
GGKAEKLHSVLKPQVQKFLD
YGFFYFNGSEVQRCQSGTVRTNCLDCLDRTNSVQAFLGLEMLAKQLEALGLAEKPQLVTR
FQEVFRSMWSVNGDSISKIYAGTGALEGKAKLKDGARSVTRTIQNNFFDSSKQEAIDVLL
LGNTLNSDLADKARALLTTGSLRVSEQTLQSASSKVLKSMCENFYKYSKPKKIRVCVGTW
NVNGGKQFRSIAFKNQTLTDWLLDAPKLAGIQEFQDKRSKPTDIFAIGFEEMVELNAGNI
VSASTTNQKLWAVELQKTISRDNKYVLLASEQLVGVCLFVFIRPQHAPFIRDVAVDTVKT
GMGGATGNKGAVAIRMLFHTTSLCFVCSHFAAGQSQVKERNEDFIEIARKLSFPMGRMLF
SHDYVFWCGDFNYRIDLPNEEVKELIRQQNWDSLIAGDQLINQKNAGQVFRGFLEGKVTF
APTYKYDLFSDDYDTSEKCRTPAWTDRVLWRRRKWPFDRSAEDLDLLNASFQDESKILYT
WTPGTLLHYGRAELKTSDH
RPVVALIDIDIFEVEAEERQNIYKEVIAVQGPPDGTVLVSI
KSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDKMWVTFLEGSSALNVLSLNGKELL
NRTITIALKSPDWIKNLEEEMSLEKISIALPSSTSSTLLGEDAEVAADF
DMEGDVDDYSA
EVEELLPQHLQPSSSSGLGTSPSSSPRTSPCQSPTISEGPVPSLPIRPSRAPSRTPGPPS
AQSSPIDAQPATPLPQKDPAQPLEPKRPPPPRPVAPPTRPAPPQRPPPPSGARSPAPTRK
EFGGIGAPPSPGVARREMEAPKSPGTTRKDNIGRSQPSPQAGLAGPGPAGYSTARPTIPP
RAGVISAPQSHARASAGRLTPESQSKTSETSKGSTFLPEPLKPQAAFPPQSSLPPPAQRL
QEPLVPVAAPMPQSGPQPNLETPPQPPPRSRSSHSLPSEASSQPQVKTNGISDGKRESPL
KIDPFEDLSFNLLAVSKAQLSVQTSPVPTPDPKRLIQLPSATQSNVLSSVSCMPTMPPIP
ARSQSQENMRSSPNPFITGLTRTNPFSDRTAAPGNPFRAKSEESEATSWFSKEEPVTISP
FPSLQPLGHNKSRASSSLDGFKDSFDLQGQSTLKISNPKGWVTFEEEEDFGVKGKSKSAC
SDLLGNQPSSFSGSNLTLNDDWNKGTNVSFCVLPSRRPPPPPVPLLPPGTSPPVDPFTTL
ASKASPTLDFTER
Sequence length 1573
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Inositol phosphate metabolism
Metabolic pathways
Phosphatidylinositol signaling system
  Synthesis of PIPs at the plasma membrane
Synthesis of IP2, IP, and Ins in the cytosol
Synthesis of IP3 and IP4 in the cytosol
Clathrin-mediated endocytosis
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
32
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Developmental and epileptic encephalopathy, 1 Likely pathogenic; Pathogenic rs1569075471 RCV000761360
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Developmental and epileptic encephalopathy, 53 Pathogenic; Likely pathogenic rs747261340, rs2145756643, rs2146047336, rs1419316294, rs1227986180, rs1040540690, rs2146213143, rs1160469053, rs2145981153, rs2146213651, rs2145769010, rs2517541465, rs2040913777, rs2517530686, rs2516760115
View all (22 more)
RCV001390943
RCV001382931
RCV001389214
RCV001387875
RCV001381958
View all (32 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Early-onset Parkinson disease 20 Pathogenic; Likely pathogenic rs747261340, rs2145756643, rs2146047336, rs1419316294, rs1227986180, rs1040540690, rs2146213143, rs1160469053, rs2145981153, rs2146213651, rs2145769010, rs2517541465, rs2040913777, rs2517530686, rs2516760115
View all (22 more)
RCV001390943
RCV001382931
RCV001389214
RCV001387875
RCV001381958
View all (32 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SYNJ1-related disorder Pathogenic rs398122403 RCV003398658
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Likely benign; Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATYPICAL JUVENILE PARKINSONISM Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Akinesia Akinesia HPO_DG
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease Alzheimer disease Pubtator 24186361, 24927707, 32493451, 33349335 Associate
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Alzheimer`s Disease Alzheimer disease GWASCAT_DG 26830138
★☆☆☆☆
Found in Text Mining only
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis BEFREE 28051077
★☆☆☆☆
Found in Text Mining only
Anarthria speech disorder Anarthria Speech Disorder HPO_DG
★☆☆☆☆
Found in Text Mining only
Attention deficit hyperactivity disorder Attention Deficit Hyperactivity Disorder HPO_DG
★☆☆☆☆
Found in Text Mining only
Atypical juvenile parkinsonism Parkinsonian disease ORPHANET_DG 23804563, 23804577
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Atypical juvenile parkinsonism Parkinsonian disease Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Autistic Disorder Autism HPO_DG
★☆☆☆☆
Found in Text Mining only
Autosomal Recessive Parkinsonism Parkinsonian disease BEFREE 31316342
★☆☆☆☆
Found in Text Mining only