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    CLVS1 clavesin 1 [ Homo sapiens (human) ]

    Gene ID: 157807, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CLVS1provided by HGNC
    Official Full Name
    clavesin 1provided by HGNC
    Primary source
    HGNC:HGNC:23139
    See related
    Ensembl:ENSG00000177182 MIM:611292; AllianceGenome:HGNC:23139
    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
    CRALBPL; RLBP1L1; C6orf212L
    Summary
    Enables phosphatidylinositol-3,5-bisphosphate binding activity. Predicted to be involved in lysosome organization. Located in endosome. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in fat (RPKM 24.7), adrenal (RPKM 7.1) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLVS1 in Genome Data Viewer
    Location:
    8q12.2-q12.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (60964848..61501629)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (61388616..61925370)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (62200529..62414188)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:61822345-61822846 Neighboring gene uncharacterized LOC105375938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:61834675-61835188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:61835189-61835702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27431 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:61841844-61842028 Neighboring gene Sharpr-MPRA regulatory region 10423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27433 Neighboring gene hCG1816373-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27439 Neighboring gene Sharpr-MPRA regulatory region 12445 Neighboring gene nuclear autoantigenic sperm protein pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:61925128-61925715 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:61925759-61926468 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:61929973-61931172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:61964453-61964975 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:61989140-61989380 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:61990570-61991243 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:61989895-61990569 Neighboring gene meiotic recombination hotspot G Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:62033015-62033646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19234 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:62075983-62076484 Neighboring gene nucleophosmin 1 pseudogene 6 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:62185690-62186311 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:62186312-62186932 Neighboring gene uncharacterized LOC105375870 Neighboring gene NANOG hESC enhancer GRCh37_chr8:62279520-62280036 Neighboring gene NANOG hESC enhancer GRCh37_chr8:62335334-62335851 Neighboring gene Sharpr-MPRA regulatory region 11405 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:62392811-62393004 Neighboring gene aspartate beta-hydroxylase Neighboring gene keratin 8 pseudogene 3 Neighboring gene RN7SK pseudogene 97

    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. Cellular retinaldehyde-binding protein-like (CRALBPL), a novel human Sec14p-like gene that is upregulated in human hepatocellular carcinomas, may be used as a marker for human hepatocellular carcinomas. Zhao S, et al. DNA Cell Biol, 2008 Mar. PMID 18271718
    2. Cloning and characterization of a novel, human cellular retinaldehyde-binding protein CRALBP-like (CRALBPL) gene. Kong YH, et al. Biotechnol Lett, 2006 Sep. PMID 16802092
    3. Steroid-sensitive nephrotic syndrome candidate gene CLVS1 regulates podocyte oxidative stress and endocytosis. Lane BM, et al. JCI Insight, 2022 Jan 25. PMID 34874915, Free PMC Article
    4. The clavesin family, neuron-specific lipid- and clathrin-binding Sec14 proteins regulating lysosomal morphology. Katoh Y, et al. J Biol Chem, 2009 Oct 2. PMID 19651769, Free PMC Article
    5. Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease. Furney SJ, et al. Mol Psychiatry, 2011 Nov. PMID 21116278, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Steroid-sensitive nephrotic syndrome candidate gene CLVS1 regulates podocyte oxidative stress and endocytosis.
      Title: Steroid-sensitive nephrotic syndrome candidate gene CLVS1 regulates podocyte oxidative stress and endocytosis.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. Clavesin protein family appears to provide a unique neuron-specific regulation of late endosome/lysosome morphology.
      Title: The clavesin family, neuron-specific lipid- and clathrin-binding Sec14 proteins regulating lysosomal morphology.
    4. CRALBPL may be used as a marker for human hepatocellular carcinomas.
      Title: Cellular retinaldehyde-binding protein-like (CRALBPL), a novel human Sec14p-like gene that is upregulated in human hepatocellular carcinomas, may be used as a marker for human hepatocellular carcinomas.
    Submit: New GeneRIF Correction

    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
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog
    Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
    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

    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

    • FLJ37248, MGC34646

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol bisphosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3,5-bisphosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in lysosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lysosome organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in clathrin-coated vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in clathrin-coated vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in trans-Golgi network membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    clavesin-1
    Names
    clathrin vesicle-associated Sec14 protein 1
    retinaldehyde-binding protein 1-like 1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_173519.3 → NP_775790.1  clavesin-1

      See identical proteins and their annotated locations for NP_775790.1

      Status: VALIDATED

      Source sequence(s)
      AC090094, AK125153, BC042617, DA217517
      Consensus CDS
      CCDS6176.1
      UniProtKB/Swiss-Prot
      B2R7M5, C8UZT3, Q8IUQ0, Q8NB32
      Related
      ENSP00000325506.4, ENST00000325897.5
      Conserved Domains (2) summary
      smart01100
      Location:51 → 97
      CRAL_TRIO_N; CRAL/TRIO, N-terminal domain
      pfam00650
      Location:125 → 274
      CRAL_TRIO; CRAL/TRIO domain

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      60964848..61501629
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024447079.2 → XP_024302847.1  clavesin-1 isoform X1

      UniProtKB/Swiss-Prot
      B2R7M5, C8UZT3, Q8IUQ0, Q8NB32
      Conserved Domains (2) summary
      smart01100
      Location:51 → 97
      CRAL_TRIO_N; CRAL/TRIO, N-terminal domain
      pfam00650
      Location:125 → 274
      CRAL_TRIO; CRAL/TRIO domain

    2. XM_017013141.2 → XP_016868630.1  clavesin-1 isoform X1

      UniProtKB/Swiss-Prot
      B2R7M5, C8UZT3, Q8IUQ0, Q8NB32
      Conserved Domains (2) summary
      smart01100
      Location:51 → 97
      CRAL_TRIO_N; CRAL/TRIO, N-terminal domain
      pfam00650
      Location:125 → 274
      CRAL_TRIO; CRAL/TRIO domain

    3. XM_017013142.3 → XP_016868631.1  clavesin-1 isoform X1

      UniProtKB/Swiss-Prot
      B2R7M5, C8UZT3, Q8IUQ0, Q8NB32
      Related
      ENSP00000428402.1, ENST00000519846.5
      Conserved Domains (2) summary
      smart01100
      Location:51 → 97
      CRAL_TRIO_N; CRAL/TRIO, N-terminal domain
      pfam00650
      Location:125 → 274
      CRAL_TRIO; CRAL/TRIO domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      61388616..61925370
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359856.1 → XP_054215831.1  clavesin-1 isoform X1

      UniProtKB/Swiss-Prot
      B2R7M5, C8UZT3, Q8IUQ0, Q8NB32

    2. XM_054359854.1 → XP_054215829.1  clavesin-1 isoform X1

      UniProtKB/Swiss-Prot
      B2R7M5, C8UZT3, Q8IUQ0, Q8NB32

    3. XM_054359855.1 → XP_054215830.1  clavesin-1 isoform X1

      UniProtKB/Swiss-Prot
      B2R7M5, C8UZT3, Q8IUQ0, Q8NB32
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IUQ0.1 GenPept UniProtKB/Swiss-Prot:Q8IUQ0

    Gene LinkOut

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

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