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SYNE4 spectrin repeat containing nuclear envelope family member 4 [ Homo sapiens (human) ]

Gene ID: 163183, updated on 11-Apr-2024

Summary

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Official Symbol
SYNE4provided by HGNC
Official Full Name
spectrin repeat containing nuclear envelope family member 4provided by HGNC
Primary source
HGNC:HGNC:26703
See related
Ensembl:ENSG00000181392 MIM:615535; AllianceGenome:HGNC:26703
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
KASH4; Nesp4; DFNB76; C19orf46
Summary
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]
Expression
Broad expression in prostate (RPKM 6.3), thyroid (RPKM 3.5) and 15 other tissues See more
Orthologs
mouse all
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Genomic context

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See SYNE4 in Genome Data Viewer
Location:
19q13.12
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (36003307..36008813, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (38549106..38554612, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (36494209..36499715, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372383 Neighboring gene Sharpr-MPRA regulatory region 3529 Neighboring gene Sharpr-MPRA regulatory region 1826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14510 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:36453209-36453373 Neighboring gene MPRA-validated peak3453 silencer Neighboring gene MPRA-validated peak3454 silencer Neighboring gene MPRA-validated peak3455 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36485053-36485552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14513 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10545 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10546 Neighboring gene succinate dehydrogenase complex assembly factor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36498887-36499428 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36499429-36499968 Neighboring gene uncharacterized LOC101927572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14514 Neighboring gene alkB homolog 6 Neighboring gene CAP-Gly domain containing linker protein 3

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
  • 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. The LINC complex is essential for hearing. Horn HF, et al. J Clin Invest, 2013 Feb. PMID 23348741, Free PMC Article
  2. Nesprin 4 is an outer nuclear membrane protein that can induce kinesin-mediated cell polarization. Roux KJ, et al. Proc Natl Acad Sci U S A, 2009 Feb 17. PMID 19164528, Free PMC Article
  3. Genetic Hearing Loss Overview. Adam MP, et al. , 1993. PMID 20301607
  4. Widespread macromolecular interaction perturbations in human genetic disorders. Sahni N, et al. Cell, 2015 Apr 23. PMID 25910212, Free PMC Article
  5. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Yang X, et al. Cell, 2016 Feb 11. PMID 26871637, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

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
Autosomal recessive nonsyndromic hearing loss 76
MedGen: C3147083 OMIM: 615540 GeneReviews: Not available
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ36445

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in establishment of epithelial cell apical/basal polarity IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in establishment of epithelial cell apical/basal polarity ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of meiotic nuclear membrane microtubule tethering complex IEA
Inferred from Electronic Annotation
more info
  
is_active_in nuclear outer membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nuclear outer membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
nesprin-4
Names
KASH domain-containing protein 4
deafness, autosomal recessive 76
nuclear envelope spectrin repeat protein 4

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.

Genomic

  1. NG_042831.1 RefSeqGene

    Range
    4981..10487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1385

mRNA and Protein(s)

  1. NM_001039876.3 → NP_001034965.1  nesprin-4 isoform 1

    See identical proteins and their annotated locations for NP_001034965.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AA991508, AC002116, AF038458, BC038360, BC052573
    Consensus CDS
    CCDS42553.1
    UniProtKB/Swiss-Prot
    A8MRS0, A8MYE3, Q7Z7L3, Q8N205
    Related
    ENSP00000316130.3, ENST00000324444.9
    Conserved Domains (1) summary
    pfam10541
    Location:368 → 404
    KASH; Nuclear envelope localization domain

  2. NM_001297735.3 → NP_001284664.1  nesprin-4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two consecutive, alternate in-frame exons in the coding region, compared to variant 1. It encodes isoform 2, which lacks an internal segment and is shorter, compared to isoform 1.
    Source sequence(s)
    AA991508, AC002116, AK093764, BC038360, BC052573
    Consensus CDS
    CCDS77285.1
    UniProtKB/Swiss-Prot
    Q8N205
    Related
    ENSP00000343152.5, ENST00000340477.9
    Conserved Domains (1) summary
    pfam10541
    Location:255 → 291
    KASH; Nuclear envelope localization domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    36003307..36008813 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047438350.1 → XP_047294306.1  nesprin-4 isoform X7

  2. XM_047438347.1 → XP_047294303.1  nesprin-4 isoform X4

  3. XM_047438345.1 → XP_047294301.1  nesprin-4 isoform X2

  4. XM_047438351.1 → XP_047294307.1  nesprin-4 isoform X8

  5. XM_047438344.1 → XP_047294300.1  nesprin-4 isoform X1

  6. XM_047438349.1 → XP_047294305.1  nesprin-4 isoform X6

  7. XM_047438346.1 → XP_047294302.1  nesprin-4 isoform X3

    Related
    ENSP00000422716.1, ENST00000490730.1

  8. XM_047438348.1 → XP_047294304.1  nesprin-4 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    38549106..38554612 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054320091.1 → XP_054176066.1  nesprin-4 isoform X7

  2. XM_054320088.1 → XP_054176063.1  nesprin-4 isoform X4

  3. XM_054320086.1 → XP_054176061.1  nesprin-4 isoform X2

  4. XM_054320092.1 → XP_054176067.1  nesprin-4 isoform X8

  5. XM_054320085.1 → XP_054176060.1  nesprin-4 isoform X1

  6. XM_054320090.1 → XP_054176065.1  nesprin-4 isoform X6

  7. XM_054320087.1 → XP_054176062.1  nesprin-4 isoform X3

  8. XM_054320089.1 → XP_054176064.1  nesprin-4 isoform X5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_153233.1: Suppressed sequence

    Description
    NM_153233.1: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N205.2 GenPept UniProtKB/Swiss-Prot:Q8N205

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