SYP (synaptophysin)

Gene Gene information from NCBI Gene database.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
Entrez ID 6855
Gene name Synaptophysin
Gene symbol SYP
Synonyms (NCBI Gene)
MRX96MRXSYPXLID96
Chromosome X
Chromosome location Xp11.23
Summary This gene encodes an integral membrane protein of small synaptic vesicles in brain and endocrine cells. The protein also binds cholesterol and is thought to direct targeting of vesicle-associated membrane protein 2 (synaptobrevin) to intracellular compart
SNPs SNP information provided by dbSNP.
4
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
Show/Hide all (4)
SNP ID Visualize variation Clinical significance Consequence
rs137852561 C>G,T Pathogenic Coding sequence variant, missense variant
rs139475570 C>T Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance Coding sequence variant, missense variant
rs145093168 C>T Conflicting-interpretations-of-pathogenicity Synonymous variant, coding sequence variant
rs201427270 G>A Conflicting-interpretations-of-pathogenicity, likely-benign Synonymous variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
70
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
Show/Hide all (70)
miRTarBase ID miRNA Experiments Reference
MIRT017945 hsa-miR-335-5p Microarray 18185580
MIRT520838 hsa-miR-410-3p HITS-CLIP 21572407
MIRT520840 hsa-miR-374a-5p HITS-CLIP 21572407
MIRT520839 hsa-miR-374b-5p HITS-CLIP 21572407
MIRT520838 hsa-miR-410-3p HITS-CLIP 21572407
Transcription factors Transcription factors information provided by TRRUST V2 database.
2
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
Show/Hide all (2)
Transcription factor Regulation Reference
PKNOX1 Activation 20864515
SP1 Unknown 12492469
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
36
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
Show/Hide all (36)
GO ID Ontology Definition Evidence Reference
GO:0005515 Function Protein binding IPI 17500595, 32296183, 32814053
GO:0006897 Process Endocytosis ISS
GO:0008021 Component Synaptic vesicle IEA
GO:0008021 Component Synaptic vesicle ISS
GO:0010807 Process Regulation of synaptic vesicle priming IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
MIM HGNC e!Ensembl
313475 11506 ENSG00000102003
Protein Protein information from UniProt database.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P08247
Protein name Synaptophysin (Major synaptic vesicle protein p38)
Protein function Possibly involved in structural functions as organizing other membrane components or in targeting the vesicles to the plasma membrane. Involved in the regulation of short-term and long-term synaptic plasticity (By similarity).
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF01284 MARVEL 21 → 221 Membrane-associating domain Domain
Tissue specificity TISSUE SPECIFICITY: Expressed in the brain, with expression in the hippocampus, the neuropil in the dentate gyrus, where expression is higher in the outer half of the molecular layer than in the inner half, and in the neuropil of CA4 and CA3 (PubMed:88385
Sequence
Sequence length 313
Interactions View interactions
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
20
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
Show/Hide Causal Diseases (2)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Intellectual disability, X-linked 96 Likely pathogenic; Pathogenic rs1557103814, rs2147882650, rs2147884161, rs137852561, rs2520590361, rs2065508863 RCV001824549
RCV000010538
RCV000010539
RCV000010541
RCV003883374
RCV002274175
Neurodevelopmental delay Likely pathogenic rs2147881303 RCV002274379
Show/Hide Unknown Diseases (3)
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Charcot-Marie-Tooth disease Conflicting classifications of pathogenicity rs139475570 RCV005625576
History of neurodevelopmental disorder Conflicting classifications of pathogenicity; Likely benign rs139475570, rs782047632 RCV000721022
RCV000721082
SYP-related disorder Likely benign rs1557102977 RCV003931514
Show/Hide Text Mining Associations (84)
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
ACTH Secreting Pituitary Adenoma Associate 31352437
Adenocarcinoma Associate 33933015
Adrenocortical Adenoma Associate 31352437
Adrenocortical Carcinoma Associate 31352437
Adrenocortical Carcinoma Stimulate 35921917
Alzheimer Disease Inhibit 22760556, 28598851
Alzheimer Disease Associate 22832605, 24927707, 30193587
Ataxia Telangiectasia Inhibit 19284608
Autism Spectrum Disorder Associate 32193494
Bipolar Disorder Inhibit 19945534