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Aliases for VPS35L Gene

Aliases for VPS35L Gene

  • VPS35 Endosomal Protein Sorting Factor Like 2 3 5
  • Esophageal Cancer Associated Protein 3
  • Esophageal Cancer-Associated Protein 4
  • Chromosome 16 Open Reading Frame 62 2
  • UPF0505 Protein C16orf62 3
  • C16orf62 3

External Ids for VPS35L Gene

Previous HGNC Symbols for VPS35L Gene

  • C16orf62

Summaries for VPS35L Gene

GeneCards Summary for VPS35L Gene

VPS35L (VPS35 Endosomal Protein Sorting Factor Like) is a Protein Coding gene. Among its related pathways are Innate Immune System.

UniProtKB/Swiss-Prot for VPS35L Gene

  • Involved in copper-dependent ATP7A trafficking between the trans-Golgi network and vesicles in the cell periphery; the function is proposed to depend on its association within the CCC complex and cooperation with the WASH complex on early endosomes. Seems not to be required for CCC complex stability (PubMed:25355947).

Additional gene information for VPS35L Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS35L Gene

Genomics for VPS35L Gene

GeneHancer (GH) Regulatory Elements for VPS35L Gene

Promoters and enhancers for VPS35L Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J019554 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 660.9 +0.6 553 2.6 HDGF PKNOX1 CLOCK SMAD1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 VPS35L RPS15A CCP110 ENSG00000263253 ENSG00000260017 ENSG00000263237 COQ7 TMC5 KNOP1 GDE1
GH16J019881 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.8 +328.6 328599 4 CTCF MXI1 ZNF777 ZNF792 RB1 BACH1 SIN3A ZIC2 KDM3A ZNF205 GPRC5B THUMPD1 VPS35L KNOP1 CCP110 LARP7P2 GC16M019876
GH16J019637 Enhancer 0.7 ENCODE dbSUPER 29.4 +83.8 83778 2.2 HDAC1 HDAC2 SCRT2 CREB1 CBFA2T2 FOS KNOP1 VPS35L IQCK GC16M019688 GC16M019687
GH16J019695 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.4 +143.2 143247 6.4 FOXA2 ARID4B FEZF1 ZNF2 ZNF48 FOS RUNX3 RXRA SSRP1 STAT3 KNOP1 VPS35L ENSG00000276571 GC16M019702
GH16J019657 Enhancer 0.6 dbSUPER 28.3 +104.7 104714 5.4 SOX13 CTCF FOXA2 HLF RAD21 SKI BCL6 NR2F6 MIXL1 VPS35L KNOP1 IQCK GC16M019688 GC16M019687
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS35L on UCSC Golden Path with GeneCards custom track

Genomic Locations for VPS35L Gene

Genomic Locations for VPS35L Gene
chr16:19,555,073-19,706,793
(GRCh38/hg38)
Size:
151,721 bases
Orientation:
Plus strand
chr16:19,566,562-19,718,115
(GRCh37/hg19)
Size:
151,554 bases
Orientation:
Plus strand

Genomic View for VPS35L Gene

Genes around VPS35L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS35L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS35L Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS35L Gene

Proteins for VPS35L Gene

  • Protein details for VPS35L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z3J2-CP062_HUMAN
    Recommended name:
    UPF0505 protein C16orf62
    Protein Accession:
    Q7Z3J2
    Secondary Accessions:
    • A8K2M1
    • O43329
    • Q69YI1
    • Q6PDA0
    • Q7L371
    • Q86W66
    • Q8WXA5
    • Q9H0L7
    • Q9H7C8

    Protein attributes for VPS35L Gene

    Size:
    963 amino acids
    Molecular mass:
    109563 Da
    Quaternary structure:
    • Interacts with COMMD1, CCDC93 and CCDC22; proposed to be a component of the CCC (COMMD/CCDC22/CCDC93) complex which contains at least COMMD1 (and possibly other COMM domain-containing proteins), CCDC22, CCDC93 and C16orf62. Interacts with WASHC1 and WASHC2C (PubMed:25355947).
    SequenceCaution:
    • Sequence=AAH14900.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAD97869.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS35L Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS35L Gene

Post-translational modifications for VPS35L Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for VPS35L Gene

Domains & Families for VPS35L Gene

Gene Families for VPS35L Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for VPS35L Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VPS35L Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q7Z3J2

UniProtKB/Swiss-Prot:

CP062_HUMAN :
  • Belongs to the UPF0505 family.
Family:
  • Belongs to the UPF0505 family.
genes like me logo Genes that share domains with VPS35L: view

Function for VPS35L Gene

Molecular function for VPS35L Gene

UniProtKB/Swiss-Prot Function:
Involved in copper-dependent ATP7A trafficking between the trans-Golgi network and vesicles in the cell periphery; the function is proposed to depend on its association within the CCC complex and cooperation with the WASH complex on early endosomes. Seems not to be required for CCC complex stability (PubMed:25355947).

Phenotypes From GWAS Catalog for VPS35L Gene

Gene Ontology (GO) - Molecular Function for VPS35L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25355947
genes like me logo Genes that share ontologies with VPS35L: view
genes like me logo Genes that share phenotypes with VPS35L: view

miRNA for VPS35L Gene

miRTarBase miRNAs that target VPS35L

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS35L Gene

Localization for VPS35L Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS35L Gene

Membrane; Single-pass membrane protein. Early endosome.

Subcellular locations from

COMPARTMENTS
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 VPS35L gene
Compartment Confidence
plasma membrane 5
endosome 4
mitochondrion 2
peroxisome 1
nucleus 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for VPS35L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IEA --
GO:0005769 early endosome IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with VPS35L: view

Pathways & Interactions for VPS35L Gene

genes like me logo Genes that share pathways with VPS35L: view

Pathways by source for VPS35L Gene

3 Reactome pathways for VPS35L Gene

Gene Ontology (GO) - Biological Process for VPS35L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006893 Golgi to plasma membrane transport IMP 25355947
GO:0015031 protein transport IEA --
GO:0043312 neutrophil degranulation TAS --
genes like me logo Genes that share ontologies with VPS35L: view

No data available for SIGNOR curated interactions for VPS35L Gene

Drugs & Compounds for VPS35L Gene

No Compound Related Data Available

Transcripts for VPS35L Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS35L Gene

No ASD Table

Relevant External Links for VPS35L Gene

GeneLoc Exon Structure for
VPS35L
ECgene alternative splicing isoforms for
VPS35L

Expression for VPS35L Gene

NURSA nuclear receptor signaling pathways regulating expression of VPS35L Gene:

VPS35L

Evidence on tissue expression from TISSUES for VPS35L Gene

  • Nervous system(4.4)
  • Heart(4.2)
  • Pancreas(4.2)
No Expression Related Data Available

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS35L Gene

Orthologs for VPS35L Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS35L Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C16orf62 34
  • 99 (a)
OneToOne
C16H16orf62 33
  • 98.93 (n)
cow
(Bos Taurus)
Mammalia C16orf62 34
  • 97 (a)
OneToOne
C25H16orf62 33
  • 91.87 (n)
dog
(Canis familiaris)
Mammalia C16orf62 34
  • 96 (a)
OneToOne
C6H16orf62 33
  • 88.89 (n)
oppossum
(Monodelphis domestica)
Mammalia C16orf62 34
  • 92 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 91 (a)
OneToMany
-- 34
  • 85 (a)
OneToMany
-- 34
  • 79 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia LOC361635 33
  • 87.57 (n)
mouse
(Mus musculus)
Mammalia 9030624J02Rik 16 34 33
  • 86.23 (n)
chicken
(Gallus gallus)
Aves C16orf62 34
  • 84 (a)
OneToOne
C14H16ORF62 33
  • 76.22 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 88 (a)
OneToMany
-- 34
  • 82 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia c16orf62 33
  • 73.63 (n)
Str.16226 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.19623 33
zebrafish
(Danio rerio)
Actinopterygii C12H16orf62 34
  • 74 (a)
OneToOne
zgc:163107 33
  • 68.89 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12356 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001150 33
  • 53.14 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG8202 34 33
  • 52.42 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F26G1.1 34
  • 19 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G50730 33
  • 43.57 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 44 (a)
OneToOne
Species where no ortholog for VPS35L was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VPS35L Gene

ENSEMBL:
Gene Tree for VPS35L (if available)
TreeFam:
Gene Tree for VPS35L (if available)

Paralogs for VPS35L Gene

No data available for Paralogs for VPS35L Gene

Variants for VPS35L Gene

Sequence variations from dbSNP and Humsavar for VPS35L Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000011122 -- 19,659,053(+) G/T intron_variant
rs1000013531 -- 19,677,351(+) G/A intron_variant
rs1000055861 -- 19,662,252(+) C/A intron_variant
rs1000068965 -- 19,634,744(+) T/C intron_variant
rs1000087345 -- 19,570,924(+) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VPS35L Gene

Variant ID Type Subtype PubMed ID
esv3435869 CNV insertion 20981092
nsv1040490 CNV gain 25217958
nsv1123016 CNV deletion 24896259
nsv1160369 CNV duplication 26073780
nsv1756 CNV insertion 18451855
nsv436835 CNV insertion 17901297
nsv520441 CNV loss 19592680
nsv571582 CNV gain 21841781
nsv571583 CNV loss 21841781
nsv833163 CNV gain 17160897

Variation tolerance for VPS35L Gene

Residual Variation Intolerance Score: 64.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.30; 53.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS35L Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS35L

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS35L Gene

Disorders for VPS35L Gene

No disorders were found for VPS35L Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot , Genatlas and External Links for VPS35L Gene

Publications for VPS35L Gene

  1. COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A. (PMID: 25355947) Phillips-Krawczak CA … Burstein E (Molecular biology of the cell 2015) 2 3 4 58
  2. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. (PMID: 10493829) Loftus BJ … Adams MD (Genomics 1999) 2 3 4 58
  3. Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling. (PMID: 28892079) McNally KE … Cullen PJ (Nature cell biology 2017) 2 3 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4 58

Products for VPS35L Gene

Sources for VPS35L Gene

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