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Aliases for SYNPO Gene

Aliases for SYNPO Gene

  • Synaptopodin 2 3 3 5
  • KIAA1029 4

External Ids for SYNPO Gene

Previous GeneCards Identifiers for SYNPO Gene

  • GC05P149963
  • GC05P150009
  • GC05P149960
  • GC05P145127

Summaries for SYNPO Gene

Entrez Gene Summary for SYNPO Gene

  • Synaptopodin is an actin-associated protein that may play a role in actin-based cell shape and motility. The name synaptopodin derives from the protein's associations with postsynaptic densities and dendritic spines and with renal podocytes (Mundel et al., 1997 [PubMed 9314539]).[supplied by OMIM, Mar 2008]

GeneCards Summary for SYNPO Gene

SYNPO (Synaptopodin) is a Protein Coding gene. Diseases associated with SYNPO include Focal Segmental Glomerulosclerosis and Nephrosclerosis. Among its related pathways are Primary Focal Segmental Glomerulosclerosis FSGS and Tight junction. GO annotations related to this gene include actin binding. An important paralog of this gene is SYNPO2.

UniProtKB/Swiss-Prot for SYNPO Gene

  • Actin-associated protein that may play a role in modulating actin-based shape and motility of dendritic spines and renal podocyte foot processes. Seems to be essential for the formation of spine apparatuses in spines of telencephalic neurons, which is involved in synaptic plasticity (By similarity).

Gene Wiki entry for SYNPO Gene

Additional gene information for SYNPO Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYNPO Gene

Genomics for SYNPO Gene

Regulatory Elements for SYNPO Gene

Enhancers for SYNPO Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05H150623 1.8 FANTOM5 Ensembl ENCODE dbSUPER 15.2 +42.5 42532 10.6 HDGF PKNOX1 SIN3A YBX1 YY1 GLIS2 ZNF143 ZNF207 FOS ATF7 MYOZ3 SYNPO ENSG00000250309 NDST1 NDST1-AS1 GC05M150601
GH05H150656 1.4 Ensembl ENCODE dbSUPER 16.4 +71.5 71474 3.6 ATF1 RB1 ZSCAN4 ZNF76 SIN3A RAD21 ZNF121 GLIS2 EGR1 ZNF143 TCOF1 HMGXB3 ZNF300 ZNF300P1 RPL7P1 SYNPO ENSG00000253852 RPS14 PDGFRB SMIM3
GH05H150460 1.6 FANTOM5 Ensembl ENCODE dbSUPER 14.1 -124.6 -124562 1.3 HDAC1 HDGF PKNOX1 TBL1XR1 RB1 SIN3A ZNF366 IKZF2 SMARCA5 ELF1 NDST1 SYNPO RPS14 NDST1-AS1 SMIM3 RBM22 ENSG00000253852 ZNF300 GC05P150482
GH05H150636 1.6 Ensembl ENCODE dbSUPER 12.2 +55.1 55125 9.9 PKNOX1 FOXA2 ARID4B SIN3A FEZF1 YY1 ZNF143 FOS REST SMARCB1 NDST1 HMGXB3 ENSG00000253852 SYNPO TCOF1 NDST1-AS1 RPS14 GC05M150601 MYOZ3
GH05H150496 1.6 Ensembl ENCODE dbSUPER 10.6 -78.0 -77978 24.1 PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF143 NDST1 TCOF1 NDST1-AS1 RPS14 HMGXB3 SYNPO ENSG00000253852 RBM22 MYOZ3 ENSG00000250309
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SYNPO on UCSC Golden Path with GeneCards custom track

Genomic Locations for SYNPO Gene

Genomic Locations for SYNPO Gene
chr5:150,586,037-150,659,230
(GRCh38/hg38)
Size:
73,194 bases
Orientation:
Plus strand
chr5:149,980,642-150,038,792
(GRCh37/hg19)

Genomic View for SYNPO Gene

Genes around SYNPO on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYNPO Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYNPO Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYNPO Gene

Proteins for SYNPO Gene

  • Protein details for SYNPO Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N3V7-SYNPO_HUMAN
    Recommended name:
    Synaptopodin
    Protein Accession:
    Q8N3V7
    Secondary Accessions:
    • A5PKZ8
    • D3DQG8
    • O15271
    • Q9UPX1

    Protein attributes for SYNPO Gene

    Size:
    929 amino acids
    Molecular mass:
    99463 Da
    Quaternary structure:
    • Interacts with BAIAP1. Interacts with actin (By similarity). Interacts (via PPxY motifs) with WWC1 (via WW domains).
    SequenceCaution:
    • Sequence=BAA82981.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SYNPO Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYNPO Gene

Post-translational modifications for SYNPO Gene

No data available for DME Specific Peptides for SYNPO Gene

Domains & Families for SYNPO Gene

Gene Families for SYNPO Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SYNPO Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYNPO Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8N3V7

UniProtKB/Swiss-Prot:

SYNPO_HUMAN :
  • Belongs to the synaptopodin family.
Family:
  • Belongs to the synaptopodin family.
genes like me logo Genes that share domains with SYNPO: view

Function for SYNPO Gene

Molecular function for SYNPO Gene

UniProtKB/Swiss-Prot Function:
Actin-associated protein that may play a role in modulating actin-based shape and motility of dendritic spines and renal podocyte foot processes. Seems to be essential for the formation of spine apparatuses in spines of telencephalic neurons, which is involved in synaptic plasticity (By similarity).

Phenotypes From GWAS Catalog for SYNPO Gene

Gene Ontology (GO) - Molecular Function for SYNPO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding ISS --
GO:0005515 protein binding IPI 18596123
genes like me logo Genes that share ontologies with SYNPO: view
genes like me logo Genes that share phenotypes with SYNPO: view

Animal Models for SYNPO Gene

MGI Knock Outs for SYNPO:

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SYNPO Gene

Localization for SYNPO Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYNPO Gene

Cytoplasm, cytoskeleton. Cell junction, tight junction. Perikaryon. Cell projection, dendritic spine. Cell junction, synapse, postsynaptic cell membrane, postsynaptic density. Cell junction, synapse. Note=Localized at the tight junction of cells. In brain, localized to the postsynaptic densities and in the perikarya. Associated with dendritic spines of a subset of synapses. {ECO:0000250 UniProtKB:Q8CC35}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYNPO gene
Compartment Confidence
cytoskeleton 5
nucleus 5
plasma membrane 4
cytosol 3
extracellular 2
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYNPO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA --
GO:0005886 plasma membrane IEA --
GO:0005923 bicellular tight junction IEA --
genes like me logo Genes that share ontologies with SYNPO: view

Pathways & Interactions for SYNPO Gene

genes like me logo Genes that share pathways with SYNPO: view

Pathways by source for SYNPO Gene

1 BioSystems pathway for SYNPO Gene
1 KEGG pathway for SYNPO Gene

Gene Ontology (GO) - Biological Process for SYNPO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008542 visual learning IEA --
GO:0032233 positive regulation of actin filament bundle assembly IBA,IEA --
GO:0048169 regulation of long-term neuronal synaptic plasticity IEA --
GO:0098886 modification of dendritic spine IDA 25164660
GO:1905355 spine apparatus assembly IEA --
genes like me logo Genes that share ontologies with SYNPO: view

No data available for SIGNOR curated interactions for SYNPO Gene

Drugs & Compounds for SYNPO Gene

(1) Drugs for SYNPO Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for SYNPO Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SYNPO: view

Transcripts for SYNPO Gene

mRNA/cDNA for SYNPO Gene

(10) REFSEQ mRNAs :
(18) Additional mRNA sequences :
(1) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SYNPO Gene

Synaptopodin:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYNPO Gene

No ASD Table

Relevant External Links for SYNPO Gene

GeneLoc Exon Structure for
SYNPO
ECgene alternative splicing isoforms for
SYNPO

Expression for SYNPO Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYNPO Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYNPO Gene

This gene is overexpressed in Muscle - Skeletal (x9.7), Heart - Left Ventricle (x4.6), and Artery - Aorta (x4.5).

Protein differential expression in normal tissues from HIPED for SYNPO Gene

This gene is overexpressed in Brain (30.6) and Frontal cortex (14.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SYNPO Gene



Protein tissue co-expression partners for SYNPO Gene

NURSA nuclear receptor signaling pathways regulating expression of SYNPO Gene:

SYNPO

SOURCE GeneReport for Unigene cluster for SYNPO Gene:

Hs.435228

mRNA Expression by UniProt/SwissProt for SYNPO Gene:

Q8N3V7-SYNPO_HUMAN
Tissue specificity: Expressed in cerebral cortex.

Evidence on tissue expression from TISSUES for SYNPO Gene

  • Nervous system(4.9)
  • Kidney(4.7)
  • Muscle(4.6)
  • Liver(4.3)
  • Heart(2.5)
genes like me logo Genes that share expression patterns with SYNPO: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SYNPO Gene

Orthologs for SYNPO Gene

This gene was present in the common ancestor of chordates.

Orthologs for SYNPO Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYNPO 33 34
  • 99 (n)
mouse
(Mus musculus)
Mammalia Synpo 33 16 34
  • 83.52 (n)
rat
(Rattus norvegicus)
Mammalia Synpo 33
  • 82.91 (n)
dog
(Canis familiaris)
Mammalia SYNPO 34
  • 72 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SYNPO 34
  • 65 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SYNPO 34
  • 45 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SYNPO 34
  • 44 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYNPO 34
  • 39 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYNPO 34
  • 35 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii SYNPO 34
  • 29 (a)
OneToOne
Species where no ortholog for SYNPO was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SYNPO Gene

ENSEMBL:
Gene Tree for SYNPO (if available)
TreeFam:
Gene Tree for SYNPO (if available)

Paralogs for SYNPO Gene

Paralogs for SYNPO Gene

genes like me logo Genes that share paralogs with SYNPO: view

Variants for SYNPO Gene

Sequence variations from dbSNP and Humsavar for SYNPO Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs1000014144 -- 150,640,309(+) GGAGG(G/T)TTCCC intron-variant, upstream-variant-2KB
rs1000021113 -- 150,591,243(+) CCTGG(C/T)GGCTG intron-variant
rs1000147253 -- 150,599,068(+) GCCAC(A/C)CATGG intron-variant
rs1000162677 -- 150,618,049(+) AGCCT(A/G)GAACC intron-variant
rs1000176017 -- 150,634,170(+) GTTAA(A/G)GTGTA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SYNPO Gene

Variant ID Type Subtype PubMed ID
nsv599960 CNV loss 21841781
nsv5064 CNV insertion 18451855
nsv5063 CNV deletion 18451855
nsv428129 CNV loss 18775914
esv3607162 CNV loss 21293372
esv33898 CNV loss 17666407
esv3349939 CNV duplication 20981092
esv2759386 CNV loss 17122850
dgv1148e214 CNV gain 21293372

Variation tolerance for SYNPO Gene

Residual Variation Intolerance Score: 48.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.78; 79.03% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SYNPO Gene

Human Gene Mutation Database (HGMD)
SYNPO
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYNPO

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYNPO Gene

Disorders for SYNPO Gene

MalaCards: The human disease database

(10) MalaCards diseases for SYNPO Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
focal segmental glomerulosclerosis
  • opitz-kaveggia syndrome
nephrosclerosis
  • renal sclerosis
galloway-mowat syndrome
  • galloway syndrome
crescentic glomerulonephritis
  • idiopathic crescentic glomerulonephritis
pauci-immune glomerulonephritis
- elite association - COSMIC cancer census association via MalaCards
Search SYNPO in MalaCards View complete list of genes associated with diseases

Relevant External Links for SYNPO

Genetic Association Database (GAD)
SYNPO
Human Genome Epidemiology (HuGE) Navigator
SYNPO
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SYNPO
genes like me logo Genes that share disorders with SYNPO: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYNPO Gene

Publications for SYNPO Gene

  1. Synaptopodin: an actin-associated protein in telencephalic dendrites and renal podocytes. (PMID: 9314539) Mundel P … Kriz W (The Journal of cell biology 1997) 2 3 4 22 60
  2. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10470851) Kikuno R … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 60
  3. Human variation in alcohol response is influenced by variation in neuronal signaling genes. (PMID: 20201926) Joslyn G … White RL (Alcoholism, clinical and experimental research 2010) 3 45 60
  4. Functional analysis of promoter mutations in the ACTN4 and SYNPO genes in focal segmental glomerulosclerosis. (PMID: 19666657) Dai S … Chen N (Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association 2010) 3 22 60
  5. KIBRA modulates directional migration of podocytes. (PMID: 18596123) Duning K … Pavenstädt H (Journal of the American Society of Nephrology : JASN 2008) 3 4 60

Products for SYNPO Gene

Sources for SYNPO Gene

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