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CLVS1 clavesin 1 [ Homo sapiens (human) ]

Gene ID: 157807, updated on 5-Mar-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, Apr 2022]
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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Location:
8q12.2-q12.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (60964848..61501629)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (61388616..61925370)
105.20220307 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
  • 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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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_2023_10

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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