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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 5-Mar-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
Predicted to enable calcium ion binding activity and chromatin binding activity. Predicted to be involved in epidermis development and lymph vessel morphogenesis. Predicted to act upstream of or within several processes, including Tie signaling pathway; lymph circulation; and lymph vessel development. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in placenta (RPKM 31.0), fat (RPKM 15.2) and 13 other tissues See more
Orthologs
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Genomic context

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Location:
9q31.3
Exon count:
48
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (110365248..110579741, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (122534766..122749357, complement)
105.20220307 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. 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
  2. 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
  3. 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
  4. SVEP1 is important for morphogenesis of lymphatic system: Possible implications in lymphedema. Michelini S, et al. Lymphology, 2021. PMID 34506084
  5. A genome-wide association study identifying SVEP1 variant as a predictor of response to tolvaptan for cirrhotic ascites. Kawaratani H, et al. Liver Int, 2021 Dec. PMID 34309184

See all (35) 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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)

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

  • 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 complement activation, classical pathway 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
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
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_2023_10

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 info@ncbi.nlm.nih.gov 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.

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