SYP synaptophysin [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYPprovided by HGNC
Official Full Name: synaptophysinprovided by HGNC
Primary source: HGNC:HGNC:11506
See related: Ensembl:ENSG00000102003 MIM:313475; AllianceGenome:HGNC:11506
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; XLID96
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: mouse all
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Genomic context

Location:: Xp11.23

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (49187815..49200193, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (48599669..48612053, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (49044268..49056652, complement)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Association between genetic polymorphisms of synaptophysin (SYP) gene and attention deficit hyperactivity disorder in Korean subjects.
Title: Association between genetic polymorphisms of synaptophysin (SYP) gene and attention deficit hyperactivity disorder in Korean subjects.
Aberrant synaptophysin expression in classic Hodgkin lymphoma.
Title: Aberrant synaptophysin expression in classic Hodgkin lymphoma.
Slowly progressive behavioral frontotemporal dementia syndrome in a family co-segregating the C9orf72 expansion and a Synaptophysin mutation.
Title: Slowly progressive behavioral frontotemporal dementia syndrome in a family co-segregating the C9orf72 expansion and a Synaptophysin mutation.
The prognostic significance of neuroendocrine markers and somatostatin receptor 2 in hepatocellular carcinoma.
Title: The prognostic significance of neuroendocrine markers and somatostatin receptor 2 in hepatocellular carcinoma.
Significance of chromogranin A and synaptophysin in medullary thyroid carcinoma.
Title: Significance of chromogranin A and synaptophysin in medullary thyroid carcinoma.
Synaptophysin expression in (V600EBRAF-)mutated advanced colorectal cancers identifies a new subgroup of tumours with worse prognosis.
Title: Synaptophysin expression in (V600EBRAF-)mutated advanced colorectal cancers identifies a new subgroup of tumours with worse prognosis.
Synaptophysin expression in lung adenocarcinoma: Persistant embryonal morphotype and/or neoplastic change?
Title: Synaptophysin expression in lung adenocarcinoma: Persistant embryonal morphotype and/or neoplastic change?
Clinicopathologic Characterization of Epithelioid Hemangioendothelioma in a Series of 62 Cases: A Proposal of Risk Stratification and Identification of a Synaptophysin-positive Aggressive Subset.
Title: Clinicopathologic Characterization of Epithelioid Hemangioendothelioma in a Series of 62 Cases: A Proposal of Risk Stratification and Identification of a Synaptophysin-positive Aggressive Subset.
Oxytocin inhibits methamphetamine-associated learning and memory alterations by regulating DNA methylation at the Synaptophysin promoter.
Title: Oxytocin inhibits methamphetamine-associated learning and memory alterations by regulating DNA methylation at the Synaptophysin promoter.
Increased expression of neurogenic factors in uterine fibroids.
Title: Increased expression of neurogenic factors in uterine fibroids.

Submit: New GeneRIF Correction See all GeneRIFs (54)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Intellectual disability, 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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

GDB:216846 (e-PCR)
- UniSTS:156218

DXS1007E (e-PCR)
- UniSTS:99643

DXS9785 (e-PCR)
- UniSTS:41590

DXS9881E (e-PCR)
- UniSTS:474537

G15886 (e-PCR)
- UniSTS:74686

DXS1007E (e-PCR)
- UniSTS:19941

RH18083 (e-PCR)
- UniSTS:54777

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SH2 domain binding	IEA Inferred from Electronic Annotation more info
enables cholesterol binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cellular response to organic substance	IEA Inferred from Electronic Annotation more info
involved_in endocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of long-term neuronal synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of neuronal synaptic plasticity	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of opioid receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of short-term neuronal synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synaptic vesicle exocytosis	IEA Inferred from Electronic Annotation more info
involved_in synaptic vesicle endocytosis	IEA Inferred from Electronic Annotation more info
involved_in synaptic vesicle maturation	NAS Non-traceable Author Statement more info	PubMed
involved_in synaptic vesicle membrane organization	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
located_in excitatory synapse	IEA Inferred from Electronic Annotation more info
located_in neuromuscular junction	IEA Inferred from Electronic Annotation more info
located_in neuron projection	IDA Inferred from Direct Assay more info	PubMed
located_in neuron projection	ISS Inferred from Sequence or Structural Similarity more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in presynaptic active zone	IBA Inferred from Biological aspect of Ancestor more info
located_in presynaptic membrane	IEA Inferred from Electronic Annotation more info
located_in synaptic vesicle	ISS Inferred from Sequence or Structural Similarity more info
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptic vesicle membrane	NAS Non-traceable Author Statement more info	PubMed
located_in terminal bouton	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: synaptophysin

Names: major synaptic vesicle protein P38

NCBI Reference Sequences (RefSeq)

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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.