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Aliases for SYNE4 Gene

Aliases for SYNE4 Gene

  • Spectrin Repeat Containing Nuclear Envelope Family Member 4 2 3 5
  • Nuclear Envelope Spectrin Repeat Protein 4 3 4
  • Deafness, Autosomal Recessive 76 2 3
  • KASH Domain-Containing Protein 4 3 4
  • C19orf46 3 4
  • KASH4 3 4
  • Chromosome 19 Open Reading Frame 46 2
  • Nesprin-4 3
  • DFNB76 3
  • Nesp4 3

External Ids for SYNE4 Gene

Previous HGNC Symbols for SYNE4 Gene

  • C19orf46
  • DFNB76

Previous GeneCards Identifiers for SYNE4 Gene

  • GC19M036496
  • GC19M036602
  • GC19M037065

Summaries for SYNE4 Gene

Entrez Gene Summary for SYNE4 Gene

  • This gene is a member of the nesprin family of genes, that encode KASH (Klarsicht, Anc-1, Syne Homology) domain-containing proteins. In addition to the KASH domain, this protein also contains a coiled-coil and leucine zipper region, a spectrin repeat, and a kinesin-1 binding region. This protein localizes to the outer nuclear membrane, and is part of the linker of nucleoskeleton and cytoskeleton (LINC) complex in the nuclear envelope. LINC complexes are formed by SUN (Sad1, UNC-84)-KASH pairs, and are thought to mechanically couple nuclear components to the cytoskeleton. Mutations in this gene have been associated with progressive high-frequency hearing loss. The absence of this protein in mice also caused hearing loss, and changes in hair cell morphology in the ears. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]

GeneCards Summary for SYNE4 Gene

SYNE4 (Spectrin Repeat Containing Nuclear Envelope Family Member 4) is a Protein Coding gene. Diseases associated with SYNE4 include Deafness, Autosomal Recessive 76 and Dfna76 Nonsyndromic Hearing Loss And Deafness. GO annotations related to this gene include actin binding.

UniProtKB/Swiss-Prot for SYNE4 Gene

  • As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning (By similarity). Behaves as a kinesin cargo, providing a functional binding site for kinesin-1 at the nuclear envelope. Hence may contribute to the establishment of secretory epithelial morphology by promoting kinesin-dependent apical migration of the centrosome and Golgi apparatus and basal localization of the nucleus (By similarity).

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYNE4 Gene

Genomics for SYNE4 Gene

Regulatory Elements for SYNE4 Gene

Enhancers for SYNE4 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
GH19G036008 0.9 ENCODE 0.7 -0.3 -306 2.0 PKNOX1 AGO1 ARID4B SIN3A DMAP1 ZNF48 YY1 GLIS2 ZNF143 SP5 ZFP82 SYNE4 ENSG00000248101
GH19G035998 1.3 Ensembl ENCODE 0.4 +9.3 9321 1.0 PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 CBX5 ZNF302 ZNF790-AS1 ZNF567 KMT2B ZNF850 ZNF345 RBM42 HAUS5 ZNF829 ZNF461 ZNF529
GH19G035994 1.1 ENCODE 0.4 +13.3 13347 2.9 HDGF PKNOX1 MLX CREB3L1 AGO1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZFP82 ZNF568 ZNF529 ZNF461 ZNF790-AS1 ZNF260 LINC01534 ZFP14 LINC00665 ZNF790
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SYNE4 on UCSC Golden Path with GeneCards custom track

Promoters for SYNE4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000109100 -507 601 SIN3A YY1 GLIS2 ZNF143 EGR2 NFYC GATAD2B KLF16 MYC DRAP1

Genomic Location for SYNE4 Gene

Chromosome:
19
Start:
36,003,000 bp from pter
End:
36,008,793 bp from pter
Size:
5,794 bases
Orientation:
Minus strand

Genomic View for SYNE4 Gene

Genes around SYNE4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYNE4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYNE4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYNE4 Gene

Proteins for SYNE4 Gene

  • Protein details for SYNE4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N205-SYNE4_HUMAN
    Recommended name:
    Nesprin-4
    Protein Accession:
    Q8N205
    Secondary Accessions:
    • A8MRS0
    • A8MYE3
    • Q7Z7L3

    Protein attributes for SYNE4 Gene

    Size:
    404 amino acids
    Molecular mass:
    43512 Da
    Quaternary structure:
    • Core component of LINC complexes which are composed of inner nuclear membrane SUN domain-containing proteins coupled to outer nuclear membrane KASH domain-containing nesprins. SUN and KASH domain-containing proteins seem to bind each other promiscuously; however, differentially expression of LINC complex constituents can give rise to specific assemblies (By similarity). Probably part of a SUN1-containing LINC complex. Interacts with kinesins KIF5B and KLC1 (By similarity).
    SequenceCaution:
    • Sequence=BAC04222.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305};

    Alternative splice isoforms for SYNE4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYNE4 Gene

Post-translational modifications for SYNE4 Gene

  • The disulfid bond with SUN1 or SUN2 is required for stability of the respective LINC complex under tensile forces.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYNE4 Gene

No data available for DME Specific Peptides for SYNE4 Gene

Domains & Families for SYNE4 Gene

Protein Domains for SYNE4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYNE4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8N205

UniProtKB/Swiss-Prot:

SYNE4_HUMAN :
  • The KASH domain, which contains a transmembrane domain, mediates the nuclear envelope targeting and is involved in the binding to SUN1 and SUN2 through recognition of their SUN domains.
  • Belongs to the nesprin family.
Domain:
  • The KASH domain, which contains a transmembrane domain, mediates the nuclear envelope targeting and is involved in the binding to SUN1 and SUN2 through recognition of their SUN domains.
Family:
  • Belongs to the nesprin family.
genes like me logo Genes that share domains with SYNE4: view

Function for SYNE4 Gene

Molecular function for SYNE4 Gene

UniProtKB/Swiss-Prot Function:
As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning (By similarity). Behaves as a kinesin cargo, providing a functional binding site for kinesin-1 at the nuclear envelope. Hence may contribute to the establishment of secretory epithelial morphology by promoting kinesin-dependent apical migration of the centrosome and Golgi apparatus and basal localization of the nucleus (By similarity).

Gene Ontology (GO) - Molecular Function for SYNE4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21516116
genes like me logo Genes that share ontologies with SYNE4: view
genes like me logo Genes that share phenotypes with SYNE4: view

Human Phenotype Ontology for SYNE4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SYNE4 Gene

MGI Knock Outs for SYNE4:

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for SYNE4 Gene

Localization for SYNE4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYNE4 Gene

Nucleus outer membrane; Single-pass type IV membrane protein. Note=Localization at the nucleus outer membrane requires the presence of SUN1. {ECO:0000250}.

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 SYNE4 gene
Compartment Confidence
nucleus 4

Gene Ontology (GO) - Cellular Components for SYNE4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005640 nuclear outer membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0031309 integral component of nuclear outer membrane ISS,IEA --
genes like me logo Genes that share ontologies with SYNE4: view

Pathways & Interactions for SYNE4 Gene

SuperPathways for SYNE4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SYNE4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045198 establishment of epithelial cell apical/basal polarity IEA,ISS --
genes like me logo Genes that share ontologies with SYNE4: view

No data available for Pathways by source and SIGNOR curated interactions for SYNE4 Gene

Drugs & Compounds for SYNE4 Gene

No Compound Related Data Available

Transcripts for SYNE4 Gene

Unigene Clusters for SYNE4 Gene

Spectrin repeat containing, nuclear envelope family member 4:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYNE4 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b
SP1: - - - -
SP2:
SP3:
SP4: - -

Relevant External Links for SYNE4 Gene

GeneLoc Exon Structure for
SYNE4
ECgene alternative splicing isoforms for
SYNE4

Expression for SYNE4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYNE4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYNE4 Gene

This gene is overexpressed in Pituitary (x5.8), Brain - Cerebellar Hemisphere (x4.5), and Brain - Cerebellum (x4.5).

NURSA nuclear receptor signaling pathways regulating expression of SYNE4 Gene:

SYNE4

SOURCE GeneReport for Unigene cluster for SYNE4 Gene:

Hs.436743

Phenotype-based relationships between genes and organs from Gene ORGANizer for SYNE4 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • inner ear
  • middle ear
  • outer ear
  • skull
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with SYNE4: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for SYNE4 Gene

Orthologs for SYNE4 Gene

This gene was present in the common ancestor of mammals.

Orthologs for SYNE4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYNE4 34 35
  • 98.76 (n)
cow
(Bos Taurus)
Mammalia SYNE4 34 35
  • 80.68 (n)
dog
(Canis familiaris)
Mammalia SYNE4 34 35
  • 80.05 (n)
rat
(Rattus norvegicus)
Mammalia LOC100911963 34
  • 76.98 (n)
mouse
(Mus musculus)
Mammalia Syne4 34 16 35
  • 76.72 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SYNE4 35
  • 54 (a)
OneToOne
Species where no ortholog for SYNE4 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • 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)
  • zebrafish (Danio rerio)

Evolution for SYNE4 Gene

ENSEMBL:
Gene Tree for SYNE4 (if available)
TreeFam:
Gene Tree for SYNE4 (if available)

Paralogs for SYNE4 Gene

No data available for Paralogs for SYNE4 Gene

Variants for SYNE4 Gene

Sequence variations from dbSNP and Humsavar for SYNE4 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs587777072 Pathogenic 36,008,267(+) TGACC(-/AT)CTCGG reference, frameshift-variant
rs200484521 Likely pathogenic 36,006,591(+) GGCCC(C/T)CAGAC reference, stop-gained
rs750797779 Likely pathogenic 36,006,809(+) GTCTC(A/G)GTAAG intron-variant, reference, stop-gained
rs199938988 Likely benign 36,003,425(+) CTGAC(A/G)CGGGC reference, missense
rs760007740 Likely benign 36,007,137(+) TGCAC(C/T)ATCCC intron-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for SYNE4 Gene

Variant ID Type Subtype PubMed ID
dgv51n68 CNV loss 17160897
esv1000212 CNV deletion 20482838

Variation tolerance for SYNE4 Gene

Residual Variation Intolerance Score: 98.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.10; 50.97% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SYNE4 Gene

Human Gene Mutation Database (HGMD)
SYNE4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYNE4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYNE4 Gene

Disorders for SYNE4 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SYNE4 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal recessive 76
  • autosomal recessive nonsyndromic deafness 76
dfna76 nonsyndromic hearing loss and deafness
  • deafness, autosomal recessive 76
autosomal recessive non-syndromic sensorineural deafness type dfnb
  • autosomal recessive isolated neurosensory deafness type dfnb
- elite association - COSMIC cancer census association via MalaCards
Search SYNE4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SYNE4_HUMAN
  • Deafness, autosomal recessive, 76 (DFNB76) [MIM:615540]: A form of non-syndromic sensorineural deafness, a disorder resulting from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DFNB76 affected individuals have onset of progressive high frequency hearing impairment between birth and 6 years of age. The hearing loss is severe at high frequencies by adulthood. {ECO:0000269 PubMed:23348741}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SYNE4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SYNE4
genes like me logo Genes that share disorders with SYNE4: view

No data available for Genatlas for SYNE4 Gene

Publications for SYNE4 Gene

  1. The LINC complex is essential for hearing. (PMID: 23348741) Horn H.F. … Avraham K.B. (J. Clin. Invest. 2013) 2 3 4 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3 64
  5. Next-generation sequencing to generate interactome datasets. (PMID: 21516116) Yu H. … Vidal M. (Nat. Methods 2011) 3 64

Products for SYNE4 Gene

Sources for SYNE4 Gene

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