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SYNPR synaptoporin [ Homo sapiens (human) ]

Gene ID: 132204, updated on 2-Nov-2024

Summary

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Official Symbol
SYNPRprovided by HGNC
Official Full Name
synaptoporinprovided by HGNC
Primary source
HGNC:HGNC:16507
See related
Ensembl:ENSG00000163630 AllianceGenome:HGNC:16507
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SPO
Summary
Predicted to be involved in modulation of chemical synaptic transmission. Predicted to be located in membrane; neuron projection; and synaptic vesicle. Predicted to be active in hippocampal mossy fiber to CA3 synapse and synaptic vesicle membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Restricted expression toward brain (RPKM 14.4) See more
Orthologs
mouse all
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Genomic context

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See SYNPR in Genome Data Viewer
Location:
3p14.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (63200604..63616924)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (63244200..63660530)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (63263984..63602600)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:63082201-63082700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:63082748-63083248 Neighboring gene long intergenic non-protein coding RNA 698 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:63121623-63122228 Neighboring gene keratin 8 pseudogene 35 Neighboring gene NANOG hESC enhancer GRCh37_chr3:63152724-63153255 Neighboring gene ubiquitin like 5 pseudogene 3 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:63329277-63329919 Neighboring gene NANOG hESC enhancer GRCh37_chr3:63429870-63430414 Neighboring gene SYNPR antisense RNA 1 Neighboring gene RNA, 5S ribosomal pseudogene 134 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:63562463-63562990 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:63631069-63631622 Neighboring gene NANOG hESC enhancer GRCh37_chr3:63637673-63638197 Neighboring gene VISTA enhancer hs1387 Neighboring gene uncharacterized LOC105377119 Neighboring gene sentan, cilia apical structure protein

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Tyrosine nitration of a synaptic protein synaptophysin contributes to amyloid beta-peptide-induced cholinergic dysfunction. Tran MH, et al. Mol Psychiatry, 2003 Apr. PMID 12740598
  2. Expression of the synaptophysin gene family is not restricted to neuronal and neuroendocrine differentiation in rat and human. Leube RE. Differentiation, 1994 May. PMID 8034131
  3. Cloning and sequence analysis of the human cDNA encoding the synaptoporin (delta), a highly conservative synaptic vesicle protein. Dai J, et al. Mol Biol Rep, 2003 Sep. PMID 12974474
  4. Synaptic vesicle protein synaptoporin is differently expressed by subpopulations of mouse hippocampal neurons. Singec I, et al. J Comp Neurol, 2002 Oct 14. PMID 12271488
  5. Genome-wide association study of maternal and inherited effects on left-sided cardiac malformations. Mitchell LE, et al. Hum Mol Genet, 2015 Jan 1. PMID 25138779, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Results from genome-wide association studies identify synaptoporin gene as one of the three susceptibility loci candidate for congenital left-sided lesions.
    Title: Genome-wide association study of maternal and inherited effects on left-sided cardiac malformations.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  3. cloning and characterization of the human cDNA that encodes the human homologue of synaptoporin
    Title: Cloning and sequence analysis of the human cDNA encoding the synaptoporin (delta), a highly conservative synaptic vesicle protein.
  4. Tyrosine nitration of synaptophysin is related to Amyloid beta induced impairment of acetylcholine release.
    Title: Tyrosine nitration of a synaptic protein synaptophysin contributes to amyloid beta-peptide-induced cholinergic dysfunction.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide association study of maternal and inherited effects on left-sided cardiac malformations.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC26651, DKFZp686G0883

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in neuron projection IEA
Inferred from Electronic Annotation
more info
  
is_active_in synaptic vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
synaptoporin

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.

mRNA and Protein(s)

  1. NM_001130003.2 → NP_001123475.1  synaptoporin isoform 1

    See identical proteins and their annotated locations for NP_001123475.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC099056, AC099545, AC104436
    Consensus CDS
    CCDS46859.1
    UniProtKB/TrEMBL
    B3KVD8
    Related
    ENSP00000418994.1, ENST00000478300.6
    Conserved Domains (1) summary
    pfam01284
    Location:16 → 216
    MARVEL; Membrane-associating domain

  2. NM_144642.5 → NP_653243.1  synaptoporin isoform 2 precursor

    See identical proteins and their annotated locations for NP_653243.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate exon in the 5' CDS, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC104436, AF411860, AL834457, DA505318
    Consensus CDS
    CCDS46860.1
    UniProtKB/Swiss-Prot
    B2R675, G5E9W4, Q8TBG9
    UniProtKB/TrEMBL
    B3KVD8
    Related
    ENSP00000295894.5, ENST00000295894.9
    Conserved Domains (1) summary
    pfam01284
    Location:73 → 196
    MARVEL; Membrane-associating domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    63200604..63616924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005731.1 → XP_016861220.1  synaptoporin isoform X1

    UniProtKB/TrEMBL
    B3KVD8

  2. XM_017005732.3 → XP_016861221.1  synaptoporin isoform X2

    UniProtKB/TrEMBL
    C9J0A2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    63244200..63660530
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345290.1 → XP_054201265.1  synaptoporin isoform X1

  2. XM_054345291.1 → XP_054201266.1  synaptoporin isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TBG9.1 GenPept UniProtKB/Swiss-Prot:Q8TBG9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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