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Aliases for CLVS1 Gene

Aliases for CLVS1 Gene

  • Clavesin 1 2 3 5
  • Clathrin Vesicle-Associated Sec14 Protein 1 3 4
  • Retinaldehyde-Binding Protein 1-Like 1 3 4
  • RLBP1L1 3 4
  • CRALBPL 3 4
  • Cellular Retinaldehyde-Binding Protein-Like 4
  • Retinaldehyde Binding Protein 1-Like 1 2
  • Clavesin-1 3

External Ids for CLVS1 Gene

Previous HGNC Symbols for CLVS1 Gene

  • RLBP1L1

Previous GeneCards Identifiers for CLVS1 Gene

  • GC08P062365
  • GC08P062201
  • GC08P057689
  • GC08P061969
  • GC08P061057

Summaries for CLVS1 Gene

GeneCards Summary for CLVS1 Gene

CLVS1 (Clavesin 1) is a Protein Coding gene. Among its related pathways are Vesicle-mediated transport and Clathrin derived vesicle budding. GO annotations related to this gene include transporter activity and phosphatidylinositol-3,5-bisphosphate binding. An important paralog of this gene is CLVS2.

UniProtKB/Swiss-Prot for CLVS1 Gene

  • Required for normal morphology of late endosomes and/or lysosomes in neurons (By similarity). Binds phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLVS1 Gene

Genomics for CLVS1 Gene

Regulatory Elements for CLVS1 Gene

Enhancers for CLVS1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08F061095 1 Ensembl ENCODE 17.2 +129.4 129361 1.3 TBP TBL1XR1 RAD21 YY1 CBX5 SCRT2 ZNF654 YY2 ZHX2 CEBPB CLVS1 CHD7 GC08M061136 GC08P061042
GH08F060997 1.6 FANTOM5 Ensembl ENCODE 14.1 +32.6 32560 3.2 TBP PKNOX1 TBL1XR1 WRNIP1 BMI1 RAD21 CBX5 ETV6 ZNF548 CREM CLVS1 CHD7 NPM1P6 GC08P061024 LOC100130298
GH08F061023 1.1 Ensembl ENCODE 12.7 +57.7 57700 2.0 ARID4B ZNF48 RAD21 YY1 GLIS2 ZNF143 ZNF654 MXD4 REST SMARCA4 CLVS1 CHD7 GC08P061024 GC08P061042
GH08F061075 1.3 Ensembl ENCODE 12.3 +110.0 110049 1.2 ATF1 PKNOX1 CREB3L1 GATA2 MBD2 MEF2D SMARCA4 PBX2 HMBOX1 KDM1A CLVS1 RN7SKP97 GC08P061042 GC08M061136
GH08F061077 1 Ensembl ENCODE 12.3 +111.6 111628 0.9 PKNOX1 ESRRA TAL1 NFRKB MAX PTRF UBTF RELA SMARCA5 L3MBTL2 CLVS1 LINC01301 GC08P061042 GC08M061136
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around CLVS1 on UCSC Golden Path with GeneCards custom track

Promoters for CLVS1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001441598 962 801 CTCF ZNF316 SMARCA4 POLR2A ZBTB11 ZBED1 ZNF407 IRF1

Genomic Location for CLVS1 Gene

60,966,438 bp from pter
61,501,645 bp from pter
535,208 bases
Plus strand

Genomic View for CLVS1 Gene

Genes around CLVS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLVS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLVS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLVS1 Gene

Proteins for CLVS1 Gene

  • Protein details for CLVS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2R7M5
    • C8UZT3
    • Q8NB32

    Protein attributes for CLVS1 Gene

    354 amino acids
    Molecular mass:
    40788 Da
    Quaternary structure:
    • Forms a complex with clathrin heavy chain and gamma-adaptin.
    • Binding to PtdIns(3,5)P2 is not required for localization.

    Alternative splice isoforms for CLVS1 Gene


neXtProt entry for CLVS1 Gene

Post-translational modifications for CLVS1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CLVS1 Gene

Domains & Families for CLVS1 Gene

Suggested Antigen Peptide Sequences for CLVS1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The CRAL-TRIO domain is required for targeting to the membrane and for binding PtdIns(3,5)P2.
  • The CRAL-TRIO domain is required for targeting to the membrane and for binding PtdIns(3,5)P2.
  • Contains 1 CRAL-TRIO domain.
genes like me logo Genes that share domains with CLVS1: view

No data available for Gene Families for CLVS1 Gene

Function for CLVS1 Gene

Molecular function for CLVS1 Gene

UniProtKB/Swiss-Prot Function:
Required for normal morphology of late endosomes and/or lysosomes in neurons (By similarity). Binds phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2).

Gene Ontology (GO) - Molecular Function for CLVS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005215 transporter activity IEA --
GO:0008289 lipid binding IEA --
GO:0080025 phosphatidylinositol-3,5-bisphosphate binding IEA,IDA 19651769
genes like me logo Genes that share ontologies with CLVS1: view
genes like me logo Genes that share phenotypes with CLVS1: view

Animal Models for CLVS1 Gene

MGI Knock Outs for CLVS1:

Animal Model Products

miRNA for CLVS1 Gene

miRTarBase miRNAs that target CLVS1

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CLVS1 Gene

Localization for CLVS1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLVS1 Gene

Golgi apparatus, trans-Golgi network membrane; Peripheral membrane protein. Cytoplasmic vesicle, clathrin-coated vesicle. Early endosome membrane; Peripheral membrane protein.

Subcellular locations from

Jensen Localization Image for CLVS1 Gene COMPARTMENTS Subcellular localization image for CLVS1 gene
Compartment Confidence
endosome 5
golgi apparatus 5
cytosol 3
nucleus 2
peroxisome 2

Gene Ontology (GO) - Cellular Components for CLVS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005768 endosome IEA,IDA 19651769
GO:0005794 Golgi apparatus IEA --
GO:0005802 trans-Golgi network IEA,ISS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with CLVS1: view

Pathways & Interactions for CLVS1 Gene

genes like me logo Genes that share pathways with CLVS1: view

Interacting Proteins for CLVS1 Gene

Gene Ontology (GO) - Biological Process for CLVS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0007040 lysosome organization IEA,ISS --
genes like me logo Genes that share ontologies with CLVS1: view

No data available for SIGNOR curated interactions for CLVS1 Gene

Transcripts for CLVS1 Gene

Unigene Clusters for CLVS1 Gene

Clavesin 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLVS1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b
SP1: - - -
SP2: -
SP5: -

Relevant External Links for CLVS1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLVS1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLVS1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLVS1 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x5.9), Brain - Nucleus accumbens (basal ganglia) (x5.5), Brain - Frontal Cortex (BA9) (x5.1), and Brain - Anterior cingulate cortex (BA24) (x4.2).

Protein differential expression in normal tissues from HIPED for CLVS1 Gene

This gene is overexpressed in Frontal cortex (53.3) and Fetal Brain (11.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CLVS1 Gene

Protein tissue co-expression partners for CLVS1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLVS1 Gene:


SOURCE GeneReport for Unigene cluster for CLVS1 Gene:


mRNA Expression by UniProt/SwissProt for CLVS1 Gene:

Tissue specificity: Expressed mainly in the brain.
genes like me logo Genes that share expression patterns with CLVS1: view

Primer Products

Orthologs for CLVS1 Gene

This gene was present in the common ancestor of animals.

Orthologs for CLVS1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLVS1 34 35
  • 99.62 (n)
(Monodelphis domestica)
Mammalia CLVS1 35
  • 96 (a)
(Bos Taurus)
Mammalia CLVS1 34 35
  • 93.5 (n)
(Canis familiaris)
Mammalia CLVS1 34 35
  • 93.41 (n)
(Rattus norvegicus)
Mammalia Clvs1 34
  • 90.77 (n)
(Mus musculus)
Mammalia Clvs1 34 16 35
  • 89.55 (n)
(Ornithorhynchus anatinus)
Mammalia CLVS1 35
  • 73 (a)
(Gallus gallus)
Aves CLVS1 34 35
  • 85.44 (n)
(Anolis carolinensis)
Reptilia CLVS1 35
  • 95 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG10657 35
  • 28 (a)
CG33966 35
  • 24 (a)
CG12926 35
  • 23 (a)
CG2663 35
  • 23 (a)
CG30339 35
  • 23 (a)
Cralbp 35
  • 23 (a)
CG1902 35
  • 21 (a)
CG31636 35
  • 21 (a)
CG33514 35
  • 21 (a)
CG10300 35
  • 20 (a)
pinta 35
  • 20 (a)
CG11550 35
  • 19 (a)
CG3823 35
  • 19 (a)
CG10301 35
  • 18 (a)
CG3191 35
  • 18 (a)
CG33965 35
  • 18 (a)
CG3091 35
  • 16 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 27 (a)
Species where no ortholog for CLVS1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for CLVS1 Gene

Gene Tree for CLVS1 (if available)
Gene Tree for CLVS1 (if available)

Paralogs for CLVS1 Gene

Paralogs for CLVS1 Gene

(5) SIMAP similar genes for CLVS1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with CLVS1: view

Variants for CLVS1 Gene

Sequence variations from dbSNP and Humsavar for CLVS1 Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
rs10046704 -- 61,281,187(+) TGAAA(A/G)TCTTC intron-variant
rs10081580 -- 61,406,732(+) cctcc(C/T)gagta intron-variant
rs10086280 -- 61,122,761(+) GTGGA(G/T)AATAC intron-variant
rs10086672 -- 61,088,902(+) GTTCA(C/T)GCCAT intron-variant
rs10086805 -- 61,089,037(+) GACCT(C/T)GTGAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLVS1 Gene

Variant ID Type Subtype PubMed ID
dgv184e180 CNV gain 20482838
esv1001731 CNV insertion 20482838
esv23432 CNV gain 19812545
esv2761429 CNV gain 21179565
esv3414209 CNV insertion 20981092
esv3576579 CNV gain 25503493
esv3617383 CNV gain 21293372
esv3617384 CNV loss 21293372
esv3617386 CNV loss 21293372
esv3617388 CNV loss 21293372
esv3617389 CNV gain 21293372
esv3617390 CNV gain 21293372
esv7324 CNV gain 19470904
esv987877 CNV insertion 20482838
esv992867 CNV insertion 20482838
nsv1029046 CNV gain 25217958
nsv1125317 OTHER inversion 24896259
nsv476325 CNV novel sequence insertion 20440878
nsv521898 CNV gain 19592680
nsv523363 CNV loss 19592680
nsv6223 CNV deletion 18451855
nsv831336 CNV gain 17160897

Variation tolerance for CLVS1 Gene

Residual Variation Intolerance Score: 17.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.87; 18.10% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLVS1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLVS1 Gene

Disorders for CLVS1 Gene

Relevant External Links for CLVS1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for CLVS1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLVS1 Gene

Publications for CLVS1 Gene

  1. The clavesin family: neuron-specific lipid- and clathrin-binding Sec14 proteins regulating lysosomal morphology. (PMID: 19651769) Katoh Y. … McPherson P.S. (J. Biol. Chem. 2009) 2 3 4 64
  2. Cloning and characterization of a novel, human cellular retinaldehyde-binding protein CRALBP-like (CRALBPL) gene. (PMID: 16802092) Kong Y.-H. … Yu L. (Biotechnol. Lett. 2006) 2 3 4 64
  3. Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease. (PMID: 21116278) Furney S.J. … . (Mol. Psychiatry 2011) 3 46 64
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for CLVS1 Gene

Sources for CLVS1 Gene

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