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    SVEP1 sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 79987, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SVEP1provided by HGNC
    Official Full Name
    sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:15985
    See related
    Ensembl:ENSG00000165124 MIM:611691; AllianceGenome:HGNC:15985
    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
    CCP22; SELOB; SEL-OB; C9orf13; POLYDOM
    Summary
    Enables integrin binding activity. Involved in negative regulation of vasoconstriction and positive regulation of platelet activation. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in placenta (RPKM 31.0), fat (RPKM 15.2) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SVEP1 in Genome Data Viewer
    Location:
    9q31.3
    Exon count:
    48
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (110365248..110579741, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (122534766..122749357, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (113127528..113342021, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987114 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_104724 Neighboring gene uncharacterized LOC124902246 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:113040078-113041277 Neighboring gene thioredoxin domain containing 8 Neighboring gene uncharacterized LOC124902245 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_104913 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_104925 Neighboring gene Sharpr-MPRA regulatory region 12709 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_104987 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105021 Neighboring gene RNA, U6 small nuclear 1039, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105134 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105151 Neighboring gene U6 spliceosomal RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:113340888-113341388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:113341389-113341889 Neighboring gene Sharpr-MPRA regulatory region 9261 Neighboring gene uncharacterized LOC124902247 Neighboring gene uncharacterized LOC105376218 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105200 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105219 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105225

    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. Identification of a nonsynonymous polymorphism in the SVEP1 gene associated with altered clinical outcomes in septic shock. Nakada TA, et al. Crit Care Med, 2015 Jan. PMID 25188548
    2. SVEP1 influences monocyte to macrophage differentiation via integrin α4β1/α9β1 and Rho/Rac signalling. Andrews SL, et al. Biochim Biophys Acta Mol Cell Res, 2023 Aug. PMID 37100352
    3. Decreased expression of SVEP1 is closely related to a cancer stem cell-like phenotype and poor prognosis in hepatocellular carcinoma. Gong WC, et al. Neoplasma, 2022 Sep. PMID 35900319
    4. Molecular and cellular characterization of SEL-OB/SVEP1 in osteogenic cells in vivo and in vitro. Shur I, et al. J Cell Physiol, 2006 Feb. PMID 16206243
    5. Effects of SVEP1 on Lung Squamous Cell Carcinoma and its Association with Tumor Mutation Burden, Prognosis, and Immune Regulation. Luo Y, et al. Comb Chem High Throughput Screen, 2023. PMID 35306983

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. EGR1 transcriptionally regulates SVEP1 to promote proliferation and migration in human coronary artery smooth muscle cells.
      Title: EGR1 transcriptionally regulates SVEP1 to promote proliferation and migration in human coronary artery smooth muscle cells.
    2. SVEP1 influences monocyte to macrophage differentiation via integrin alpha4beta1/alpha9beta1 and Rho/Rac signalling.
      Title: SVEP1 influences monocyte to macrophage differentiation via integrin α4β1/α9β1 and Rho/Rac signalling.
    3. Effects of SVEP1 on Lung Squamous Cell Carcinoma and its Association with Tumor Mutation Burden, Prognosis, and Immune Regulation.
      Title: Effects of SVEP1 on Lung Squamous Cell Carcinoma and its Association with Tumor Mutation Burden, Prognosis, and Immune Regulation.
    4. Decreased expression of SVEP1 is closely related to a cancer stem cell-like phenotype and poor prognosis in hepatocellular carcinoma.
      Title: Decreased expression of SVEP1 is closely related to a cancer stem cell-like phenotype and poor prognosis in hepatocellular carcinoma.
    5. The integrin ligand SVEP1 regulates GPCR-mediated vasoconstriction via integrins alpha9beta1 and alpha4beta1.
      Title: The integrin ligand SVEP1 regulates GPCR-mediated vasoconstriction via integrins α9β1 and α4β1.
    6. SVEP1 is important for morphogenesis of lymphatic system: Possible implications in lymphedema.
      Title: SVEP1 is important for morphogenesis of lymphatic system: Possible implications in lymphedema.
    7. A genome-wide association study identifying SVEP1 variant as a predictor of response to tolvaptan for cirrhotic ascites.
      Title: A genome-wide association study identifying SVEP1 variant as a predictor of response to tolvaptan for cirrhotic ascites.
    8. Functional investigation of the coronary artery disease gene SVEP1.
      Title: Functional investigation of the coronary artery disease gene SVEP1.
    9. SVEP1 is a human coronary artery disease locus that promotes atherosclerosis.
      Title: SVEP1 is a human coronary artery disease locus that promotes atherosclerosis.
    10. SVEP1 as a Genetic Modifier of TEK-Related Primary Congenital Glaucoma.
      Title: SVEP1 as a Genetic Modifier of TEK-Related Primary Congenital Glaucoma.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder.
    EBI GWAS Catalog
    Exploring genome-wide - dietary heme iron intake interactions and the risk of type 2 diabetes.
    EBI GWAS Catalog
    Genome-wide association study of lung function decline in adults with and without asthma.
    EBI GWAS Catalog
    Joint influence of small-effect genetic variants on human longevity.
    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

    • FLJ16013, FLJ90719

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables integrin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables integrin binding involved in cell-matrix adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Tie signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell-matrix adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in epidermis development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lymph circulation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lymph vessel morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of vasoconstriction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of platelet activation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tight junction organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular region ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1
    Names
    CCP module-containing protein 22
    selectin-like osteoblast-derived protein
    selectin-like protein
    serologically defined breast cancer antigen NY-BR-38

    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_153366.4 → NP_699197.3  sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 precursor

      See identical proteins and their annotated locations for NP_699197.3

      Status: VALIDATED

      Source sequence(s)
      AK075200, AL158158, AL832416, AY243503, BC030816, BF368046, BX106110, CX165144, DR008048, DV080389
      Consensus CDS
      CCDS48004.1
      UniProtKB/Swiss-Prot
      Q0P675, Q4LDE5, Q5D213, Q5T938, Q5VTE4, Q5VTE5, Q7Z387, Q7Z3G3, Q8NBT9, Q96JU7, Q9H284, Q9H8J9
      UniProtKB/TrEMBL
      Q5JB40
      Related
      ENSP00000363593.2, ENST00000374469.6
      Conserved Domains (12) summary
      cd00033
      Location:438 → 494
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      PHA02639
      Location:2714 → 2887
      PHA02639; EEV host range protein; Provisional
      PHA02817
      Location:1958 → 2079
      PHA02817; EEV Host range protein; Provisional
      PHA02831
      Location:2280 → 2436
      PHA02831; EEV host range protein; Provisional
      smart00179
      Location:1745 → 1783
      EGF_CA; Calcium-binding EGF-like domain
      PHA02927
      Location:1789 → 2017
      PHA02927; secreted complement-binding protein; Provisional
      cd00054
      Location:1383 → 1419
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam00084
      Location:1628 → 1685
      Sushi; Sushi repeat (SCR repeat)
      pfam00092
      Location:84 → 258
      VWA; von Willebrand factor type A domain
      pfam07699
      Location:1005 → 1052
      Ephrin_rec_like; Putative ephrin-receptor like
      cl03620
      Location:560 → 642
      DUF5011; Domain of unknown function (DUF5011)
      cl22861
      Location:1424 → 1622
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      110365248..110579741 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      122534766..122749357 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_024500.2: Suppressed sequence

      Description
      NM_024500.2: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4LDE5.3 GenPept UniProtKB/Swiss-Prot:Q4LDE5

    Gene LinkOut

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

    Chemical Information
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