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    SVIP small VCP interacting protein [ Homo sapiens (human) ]

    Gene ID: 258010, updated on 3-Nov-2024

    Summary

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    Official Symbol
    SVIPprovided by HGNC
    Official Full Name
    small VCP interacting proteinprovided by HGNC
    Primary source
    HGNC:HGNC:25238
    See related
    Ensembl:ENSG00000198168 MIM:620965; AllianceGenome:HGNC:25238
    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
    Summary
    Endoplasmic reticulum-associated degradation (ERAD) is the pathway by which misfolded proteins in the endoplasmic reticulum are targeted to the proteasome for degradation. Multiple specialized proteins interact with one another during ERAD to complete this process. The protein encoded by this gene is an inhibitor of ERAD, functioning to disrupt the interaction of these protein components. This downregulation of ERAD may be needed to protect the cell from overactive protein degradation. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]
    Expression
    Ubiquitous expression in thyroid (RPKM 21.5), stomach (RPKM 10.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SVIP in Genome Data Viewer
    Location:
    11p14.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (22818927..22829801, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (22939594..22950463, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (22840473..22851347, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4534 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:22646933-22647832 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:22656570-22657334 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3206 Neighboring gene FA complementation group F Neighboring gene growth arrest specific 2 Neighboring gene RNA, 5S ribosomal pseudogene 338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4538 Neighboring gene Sharpr-MPRA regulatory region 5411 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:22813641-22814840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3207 Neighboring gene long intergenic non-protein coding RNA 2718 Neighboring gene Sharpr-MPRA regulatory region 14851 Neighboring gene coiled-coil domain containing 179 Neighboring gene uncharacterized LOC124902646 Neighboring gene NANOG hESC enhancer GRCh37_chr11:22944198-22944709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:23054822-23055322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:23055323-23055823

    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. Differential Expression and Function of SVIP in Breast Cancer Cell Lines and In Silico Analysis of Its Expression and Prognostic Potential in Human Breast Cancer. Atalay Şahar E, et al. Cells, 2023 May 11. PMID 37408196, Free PMC Article
    2. Regulation of ER-associated degradation via p97/VCP-interacting motif. Ballar P, et al. Biochem Soc Trans, 2008 Oct. PMID 18793143
    3. A Determination of p97/VCP (Valosin Containing Protein) and SVIP (Small VCP Interacting Protein) Expression Patterns in Human Testis. Arıcı A, et al. Medicina (Kaunas), 2023 Jun 3. PMID 37374283, Free PMC Article
    4. SVIP alleviates CCl(4)-induced liver fibrosis via activating autophagy and protecting hepatocytes. Jia D, et al. Cell Death Dis, 2019 Jan 25. PMID 30683843, Free PMC Article
    5. Structure and expression of a novel compact myelin protein - small VCP-interacting protein (SVIP). Wu J, et al. Biochem Biophys Res Commun, 2013 Oct 11. PMID 24055875, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Differential Expression and Function of SVIP in Breast Cancer Cell Lines and In Silico Analysis of Its Expression and Prognostic Potential in Human Breast Cancer.
      Title: Differential Expression and Function of SVIP in Breast Cancer Cell Lines and In Silico Analysis of Its Expression and Prognostic Potential in Human Breast Cancer.
    2. A Determination of p97/VCP (Valosin Containing Protein) and SVIP (Small VCP Interacting Protein) Expression Patterns in Human Testis.
      Title: A Determination of p97/VCP (Valosin Containing Protein) and SVIP (Small VCP Interacting Protein) Expression Patterns in Human Testis.
    3. SVIP is a molecular determinant of lysosomal dynamic stability, neurodegeneration and lifespan.
      Title: SVIP is a molecular determinant of lysosomal dynamic stability, neurodegeneration and lifespan.
    4. Overexpression of SVIP can protect HepG2 cells from the toxicity of CCl4, which could be enhanced by starvation.
      Title: SVIP alleviates CCl(4)-induced liver fibrosis via activating autophagy and protecting hepatocytes.
    5. overexpression of gp78 or SVIP suppression may eliminate the toxic gain of function associated with polymerization of ZAAT, thus providing a potential new therapeutic approach to the treatment of alpha-1 antitrypsin deficiency
      Title: SVIP regulates Z variant alpha-1 antitrypsin retro-translocation by inhibiting ubiquitin ligase gp78.
    6. the interactions between P97 and these motifs, including VCP-binding motif (VBM) and VCP-interacting motif (VIM). The solution structures of the VBM motif from HRD1 and the VIM motif from SVIP are both comprised mainly of a single alpha-helix.
      Title: Structural and mechanistic insights into the arginine/lysine-rich peptide motifs that interact with P97/VCP.
    7. A major portion of SVIP is intrinsically disordered in solution.
      Title: Structure and expression of a novel compact myelin protein - small VCP-interacting protein (SVIP).
    8. SVIP plays a regulatory role in p97 subcellular localization and is a novel regulator of autophagy.
      Title: SVIP induces localization of p97/VCP to the plasma and lysosomal membranes and regulates autophagy.
    9. SVIP is an endogenous inhibitor of ERAD that acts through regulating the assembly of the gp78-p97/VCP-Derlin1 complex.
      Title: Identification of SVIP as an endogenous inhibitor of endoplasmic reticulum-associated degradation.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
    EBI GWAS Catalog
    Integrated Genome-wide Association, Coexpression Network, and Expression Single Nucleotide Polymorphism Analysis Identifies Novel Pathway in Allergic Rhinitis.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp313A2432

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATPase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of ERAD pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of VCP-NPL4-UFD1 AAA ATPase complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of protein-containing complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of retrograde protein transport, ER to cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of retrograde protein transport, ER to cytosol IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of autophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of protein lipidation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in secretory granule membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in smooth endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in tertiary granule membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    small VCP/p97-interacting protein

    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_001320340.1 → NP_001307269.1  small VCP/p97-interacting protein isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes one of two longer isoforms (1).
      Source sequence(s)
      AC006299, AF527534, BI826588
      UniProtKB/Swiss-Prot
      Q8NHG7
      Conserved Domains (1) summary
      pfam15811
      Location:17 → 75
      SVIP; Small VCP/p97-interacting protein

    2. NM_001320341.3 → NP_001307270.1  small VCP/p97-interacting protein isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and uses an alternate splice junction in the 3' end compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus and a longer and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AA347778, AC006299
      Conserved Domains (1) summary
      pfam15811
      Location:1 → 73
      SVIP; Small VCP/p97-interacting protein

    3. NM_001320342.3 → NP_001307271.1  small VCP/p97-interacting protein isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and uses an alternate splice junction in the 3' end compared to variant 1. The resulting isoform (4) has a shorter and distinct N-terminus and a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC006299, AF527534, DB135755, DB466086
      UniProtKB/Swiss-Prot
      Q8NHG7
      Conserved Domains (1) summary
      pfam15811
      Location:1 → 73
      SVIP; Small VCP/p97-interacting protein

    4. NM_148893.3 → NP_683691.1  small VCP/p97-interacting protein isoform 3

      See identical proteins and their annotated locations for NP_683691.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC006299, AF527534
      Consensus CDS
      CCDS41627.1
      UniProtKB/Swiss-Prot
      Q8NHG7
      Related
      ENSP00000346130.4, ENST00000354193.5
      Conserved Domains (1) summary
      pfam15811
      Location:1 → 73
      SVIP; Small VCP/p97-interacting protein

    RNA

    1. NR_135213.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC006299, AF527534, BF219509, BG531443, DA306370

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      22818927..22829801 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      22939594..22950463 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NHG7.1 GenPept UniProtKB/Swiss-Prot:Q8NHG7

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