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Aliases for CLVS2 Gene

Aliases for CLVS2 Gene

  • Clavesin 2 2 3 5
  • Clathrin Vesicle-Associated Sec14 Protein 2 3 4
  • Retinaldehyde Binding Protein 1-Like 2 2 3
  • C6orf212 3 4
  • C6orf213 3 4
  • RLBP1L2 3 4
  • Retinaldehyde-Binding Protein 1-Like 2 4
  • Chromosome 6 Open Reading Frame 212 2
  • Chromosome 6 Open Reading Frame 213 2
  • BA160A10.4 3
  • Clavesin-2 3

External Ids for CLVS2 Gene

Previous HGNC Symbols for CLVS2 Gene

  • C6orf212
  • C6orf213
  • RLBP1L2

Previous GeneCards Identifiers for CLVS2 Gene

  • GC06P123360
  • GC06P120894

Summaries for CLVS2 Gene

Entrez Gene Summary for CLVS2 Gene

  • This gene encodes a protein that belongs to the SEC14/CRAL-TRIO family of proteins. A similar protein in rat is thought to function in the endosomal pathway between early endosomes and mature lysosomes. [provided by RefSeq, Aug 2013]

GeneCards Summary for CLVS2 Gene

CLVS2 (Clavesin 2) is a Protein Coding gene. Diseases associated with CLVS2 include Cataract 8, Multiple Types. Among its related pathways are Clathrin derived vesicle budding and Vesicle-mediated transport. Gene Ontology (GO) annotations related to this gene include transporter activity and phosphatidylinositol-3,5-bisphosphate binding. An important paralog of this gene is CLVS1.

UniProtKB/Swiss-Prot for CLVS2 Gene

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

Additional gene information for CLVS2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLVS2 Gene

Genomics for CLVS2 Gene

GeneHancer (GH) Regulatory Elements for CLVS2 Gene

Promoters and enhancers for CLVS2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J122997 Promoter/Enhancer 1.2 EPDnew ENCODE 650.7 +0.2 211 0.1 MXI1 ZNF777 ZNF2 ZNF335 GLIS2 POLR2A ZBTB48 PRDM10 ZNF600 ZBTB20 CLVS2 GC06P123069
GH06J122996 Enhancer 0.7 ENCODE 650.7 +0.7 690 0.1 ZIC2 ZNF2 YY1 ZNF335 CTBP1 GLIS2 ZNF366 PRDM10 KLF8 ZBTB20 CLVS2 GC06P123069
GH06J123055 Enhancer 0.9 ENCODE 8.3 +60.9 60915 2.2 FOXA2 ARID4B ETS1 YY1 TCF12 ATF7 NFKBIZ RXRA SP5 MIER2 CLVS2 GC06P123069
GH06J123029 Enhancer 0.2 FANTOM5 17.9 +33.4 33375 0.3 CLVS2 GC06P123069
GH06J123090 Enhancer 0.8 Ensembl ENCODE 4.3 +95.5 95505 2.5 SMARCE1 NCOA3 PKNOX1 FOXA2 RFX1 DPF2 FEZF1 FOXA1 SP1 GATA3 CLVS2 GC06P123069 LOC105377984
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CLVS2 on UCSC Golden Path with GeneCards custom track

Genomic Locations for CLVS2 Gene

Genomic Locations for CLVS2 Gene
76,957 bases
Plus strand

Genomic View for CLVS2 Gene

Genes around CLVS2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLVS2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLVS2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLVS2 Gene

Proteins for CLVS2 Gene

  • Protein details for CLVS2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B3KTG5
    • B4DHL0
    • C8UZT4
    • Q5SYC0

    Protein attributes for CLVS2 Gene

    327 amino acids
    Molecular mass:
    38000 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 CLVS2 Gene


neXtProt entry for CLVS2 Gene

Post-translational modifications for CLVS2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLVS2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLVS2 Gene

Domains & Families for CLVS2 Gene

Gene Families for CLVS2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for CLVS2 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.
genes like me logo Genes that share domains with CLVS2: view

Function for CLVS2 Gene

Molecular function for CLVS2 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).

Phenotypes From GWAS Catalog for CLVS2 Gene

Gene Ontology (GO) - Molecular Function for CLVS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008289 lipid binding IEA --
GO:0080025 phosphatidylinositol-3,5-bisphosphate binding IDA 19651769
genes like me logo Genes that share ontologies with CLVS2: view
genes like me logo Genes that share phenotypes with CLVS2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CLVS2

Clone Products

  • Addgene plasmids for CLVS2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CLVS2 Gene

Localization for CLVS2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLVS2 Gene

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

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLVS2 gene
Compartment Confidence
golgi apparatus 5
endosome 5
cytosol 3
nucleus 2
extracellular 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for CLVS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IDA 19651769
GO:0005794 Golgi apparatus IEA --
GO:0005802 trans-Golgi network ISS --
GO:0016020 membrane IEA --
GO:0030136 clathrin-coated vesicle ISS --
genes like me logo Genes that share ontologies with CLVS2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLVS2 Gene

Pathways & Interactions for CLVS2 Gene

genes like me logo Genes that share pathways with CLVS2: view

Gene Ontology (GO) - Biological Process for CLVS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007040 lysosome organization ISS --
genes like me logo Genes that share ontologies with CLVS2: view

No data available for SIGNOR curated interactions for CLVS2 Gene

Drugs & Compounds for CLVS2 Gene

No Compound Related Data Available

Transcripts for CLVS2 Gene

mRNA/cDNA for CLVS2 Gene

(3) Selected AceView cDNA sequences:
(4) Additional mRNA sequences :
(1) REFSEQ mRNAs :
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLVS2 Gene

Clavesin 2:
Representative Sequences:

Clone Products

  • Addgene plasmids for CLVS2

Alternative Splicing Database (ASD) splice patterns (SP) for CLVS2 Gene

No ASD Table

Relevant External Links for CLVS2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLVS2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLVS2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLVS2 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x9.5), Brain - Cerebellum (x9.2), Brain - Frontal Cortex (BA9) (x4.5), and Brain - Anterior cingulate cortex (BA24) (x4.4).

Protein differential expression in normal tissues from HIPED for CLVS2 Gene

This gene is overexpressed in Fetal Brain (23.5), Frontal cortex (20.1), Retina (12.2), and Prostate (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLVS2 Gene

Protein tissue co-expression partners for CLVS2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLVS2 Gene:


SOURCE GeneReport for Unigene cluster for CLVS2 Gene:


Evidence on tissue expression from TISSUES for CLVS2 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with CLVS2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLVS2 Gene

Orthologs for CLVS2 Gene

This gene was present in the common ancestor of animals.

Orthologs for CLVS2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLVS2 34 33
  • 99.8 (n)
(Ornithorhynchus anatinus)
Mammalia CLVS2 34
  • 95 (a)
(Canis familiaris)
Mammalia CLVS2 34 33
  • 94.29 (n)
(Bos Taurus)
Mammalia CLVS2 34 33
  • 93.58 (n)
(Monodelphis domestica)
Mammalia CLVS2 34
  • 93 (a)
(Mus musculus)
Mammalia Clvs2 16 34 33
  • 90.72 (n)
(Gallus gallus)
Aves CLVS2 34 33
  • 86.44 (n)
(Anolis carolinensis)
Reptilia CLVS2 34
  • 91 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clvs2 33
  • 79.51 (n)
(Danio rerio)
Actinopterygii clvs2 34 33
  • 78.7 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008133 33
  • 55.66 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG10657 34
  • 27 (a)
CG33966 34
  • 25 (a)
CG31636 34
  • 23 (a)
Cralbp 34
  • 23 (a)
CG33514 34
  • 23 (a)
CG12926 34
  • 22 (a)
CG2663 34
  • 21 (a)
CG30339 34
  • 21 (a)
CG1902 34
  • 21 (a)
pinta 34
  • 20 (a)
CG10300 34
  • 19 (a)
CG3191 34
  • 19 (a)
CG3823 34
  • 19 (a)
CG33965 34
  • 18 (a)
CG10301 34
  • 18 (a)
CG3091 34
  • 17 (a)
CG11550 34
  • 17 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 25 (a)
Species where no ortholog for CLVS2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • rat (Rattus norvegicus)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLVS2 Gene

Gene Tree for CLVS2 (if available)
Gene Tree for CLVS2 (if available)
Evolutionary constrained regions (ECRs) for CLVS2: view image

Paralogs for CLVS2 Gene

Paralogs for CLVS2 Gene

(5) SIMAP similar genes for CLVS2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CLVS2: view

Variants for CLVS2 Gene

Sequence variations from dbSNP and Humsavar for CLVS2 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000007431 -- 123,036,935(+) G/A/T intron_variant
rs1000007766 -- 123,077,605(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000027908 -- 122,994,106(+) A/G 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000038524 -- 123,037,216(+) T/C intron_variant
rs1000108653 -- 123,001,292(+) ATTGTAAAGA/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CLVS2 Gene

Variant ID Type Subtype PubMed ID
esv2671436 CNV deletion 23128226
esv2732655 CNV deletion 23290073
esv3540403 CNV deletion 23714750
esv3610621 CNV loss 21293372
nsv474462 CNV novel sequence insertion 20440878
nsv955900 CNV deletion 24416366

Variation tolerance for CLVS2 Gene

Residual Variation Intolerance Score: 20.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.73; 15.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLVS2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLVS2 Gene

Disorders for CLVS2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CLVS2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
cataract 8, multiple types
  • ctrct8
- elite association - COSMIC cancer census association via MalaCards
Search CLVS2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLVS2

genes like me logo Genes that share disorders with CLVS2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLVS2 Gene

Publications for CLVS2 Gene

  1. The clavesin family, neuron-specific lipid- and clathrin-binding Sec14 proteins regulating lysosomal morphology. (PMID: 19651769) Katoh Y … McPherson PS (The Journal of biological chemistry 2009) 2 3 4 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C … Emili A (Nature 2015) 3 58
  4. A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. (PMID: 22219177) Tao S … Sun J (Carcinogenesis 2012) 3 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 4 58

Products for CLVS2 Gene

Sources for CLVS2 Gene

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