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SYP synaptophysin [ Homo sapiens (human) ]

Gene ID: 6855, updated on 24-Nov-2020

Summary

Official Symbol
SYPprovided by HGNC
Official Full Name
synaptophysinprovided by HGNC
Primary source
HGNC:HGNC:11506
See related
Ensembl:ENSG00000102003 MIM:313475
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MRX96; MRXSYP
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 compartments. Mutations in this gene are associated with an X-linked form of cognitive disability. [provided by RefSeq, Jul 2017]
Expression
Biased expression in brain (RPKM 226.8) and adrenal (RPKM 21.1) See more
Orthologs

Genomic context

See SYP in Genome Data Viewer
Location:
Xp11.23
Exon count:
7
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (49187815..49200193, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (49044263..49056661, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene MAGI family member, X-linked Neighboring gene prickle planar cell polarity protein 3 Neighboring gene proteolipid protein 2 Neighboring gene SYP antisense RNA 1 Neighboring gene calcium voltage-gated channel subunit alpha1 F Neighboring gene heat shock protein family B (small) member 1 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mental retardation, X-linked 96
MedGen: C3275408 OMIM: 300802 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2018-09-26)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated (2018-09-26)

ClinGen Genome Curation PagePubMed

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat Creatine inhibits HIV-1 Tat-induced downregulation of synaptophysin in neuron cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SH2 domain binding IEA
Inferred from Electronic Annotation
more info
 
cholesterol binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein self-association TAS
Traceable Author Statement
more info
PubMed 
syntaxin-1 binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
cellular response to organic substance IEA
Inferred from Electronic Annotation
more info
 
endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of long-term neuronal synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of neuronal synaptic plasticity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of opioid receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of short-term neuronal synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic vesicle endocytosis IEA
Inferred from Electronic Annotation
more info
 
synaptic vesicle maturation NAS
Non-traceable Author Statement
more info
PubMed 
synaptic vesicle membrane organization NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
excitatory synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of synaptic vesicle membrane NAS
Non-traceable Author Statement
more info
PubMed 
neuromuscular junction IEA
Inferred from Electronic Annotation
more info
 
neuron projection IDA
Inferred from Direct Assay
more info
PubMed 
neuron projection ISS
Inferred from Sequence or Structural Similarity
more info
 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
presynaptic active zone IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
presynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
synaptic vesicle ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
terminal bouton IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
synaptophysin
Names
major synaptic vesicle protein P38

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_012532.1 RefSeqGene

    Range
    5001..17397
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_003179.3NP_003170.1  synaptophysin

    See identical proteins and their annotated locations for NP_003170.1

    Status: REVIEWED

    Source sequence(s)
    BC064550, X06389
    Consensus CDS
    CCDS14321.1
    UniProtKB/Swiss-Prot
    P08247
    Related
    ENSP00000263233.4, ENST00000263233.8
    Conserved Domains (1) summary
    pfam01284
    Location:22221
    MARVEL; Membrane-associating domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    49187815..49200193 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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