CLEC16A Gene (Protein Coding)

C-Type Lectin Domain Containing 16A

GC16P010944
GIFtS:
38
This gene encodes a member of the C-type lectin domain containing family. Single nucleotide polymorphisms in introns of this gene have been associated with diabetes mellitus, multiple sclerosis and rheumatoid arthritis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011] See more...

Aliases for CLEC16A Gene

Aliases for CLEC16A Gene

  • C-Type Lectin Domain Containing 16A 2 3 5
  • C-Type Lectin Domain Family 16 Member A 2 3 4
  • KIAA0350 2 3 4
  • Protein CLEC16A 3 4
  • Gop-1 2 3
  • C-Type Lectin Domain Family 16, Member A 2
  • CLEC16A 5

External Ids for CLEC16A Gene

Previous HGNC Symbols for CLEC16A Gene

  • KIAA0350

Previous GeneCards Identifiers for CLEC16A Gene

  • GC16P010945
  • GC16P011038
  • GC16P010955

Summaries for CLEC16A Gene

Entrez Gene Summary for CLEC16A Gene

  • This gene encodes a member of the C-type lectin domain containing family. Single nucleotide polymorphisms in introns of this gene have been associated with diabetes mellitus, multiple sclerosis and rheumatoid arthritis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

GeneCards Summary for CLEC16A Gene

CLEC16A (C-Type Lectin Domain Containing 16A) is a Protein Coding gene. Diseases associated with CLEC16A include Primary Progressive Multiple Sclerosis and Multiple Sclerosis.

UniProtKB/Swiss-Prot Summary for CLEC16A Gene

  • Regulator of mitophagy through the upstream regulation of the RNF41/NRDP1-PRKN pathway. Mitophagy is a selective form of autophagy necessary for mitochondrial quality control. The RNF41/NRDP1-PRKN pathway regulates autophagosome-lysosome fusion during late mitophagy. May protect RNF41/NRDP1 from proteosomal degradation, RNF41/NRDP1 which regulates proteosomal degradation of PRKN. Plays a key role in beta cells functions by regulating mitophagy/autophagy and mitochondrial health.

Gene Wiki entry for CLEC16A Gene

Additional gene information for CLEC16A Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLEC16A Gene

Genomics for CLEC16A Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CLEC16A Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLEC16A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLEC16A

Top Transcription factor binding sites by QIAGEN in the CLEC16A gene promoter:
  • AREB6
  • Egr-4
  • Ik-2
  • Pax-5
  • POU2F1
  • POU2F1a
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)

Genomic Locations for CLEC16A Gene

Latest Assembly
chr16:10,944,539-11,193,272
(GRCh38/hg38)
Size:
248,734 bases
Orientation:
Plus strand

Previous Assembly
chr16:11,038,421-11,276,043
(GRCh37/hg19 by Entrez Gene)
Size:
237,623 bases
Orientation:
Plus strand

chr16:11,038,345-11,276,046
(GRCh37/hg19 by Ensembl)
Size:
237,702 bases
Orientation:
Plus strand

Genomic View for CLEC16A Gene

Genes around CLEC16A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLEC16A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLEC16A Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CLEC16A Gene

Proteins for CLEC16A Gene

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  • Protein details for CLEC16A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q2KHT3-CL16A_HUMAN
    Recommended name:
    Protein CLEC16A
    Protein Accession:
    Q2KHT3
    Secondary Accessions:
    • O15058
    • Q6ZTB2

    Protein attributes for CLEC16A Gene

    Size:
    1053 amino acids
    Molecular mass:
    117715 Da
    Quaternary structure:
    • Interacts with RNF41/NRDP1.
    SequenceCaution:
    • Sequence=BAA20807.3; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for CLEC16A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLEC16A Gene

Protein Expression for CLEC16A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CLEC16A Gene

  • Ubiquitination at Lys445
  • Modification sites at PhosphoSitePlus

Other Protein References for CLEC16A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLEC16A Gene

Domains & Families for CLEC16A Gene

Gene Families for CLEC16A Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for CLEC16A Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CLEC16A Gene

GenScript: Design optimal peptide antigens:
  • Protein CLEC16A (CL16A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q2KHT3

UniProtKB/Swiss-Prot:

CL16A_HUMAN :
  • Belongs to the CLEC16A/gop-1 family.
Family:
  • Belongs to the CLEC16A/gop-1 family.
genes like me logo Genes that share domains with CLEC16A: view

Function for CLEC16A Gene

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  6. Cell Lines for research

Molecular function for CLEC16A Gene

UniProtKB/Swiss-Prot Function:
Regulator of mitophagy through the upstream regulation of the RNF41/NRDP1-PRKN pathway. Mitophagy is a selective form of autophagy necessary for mitochondrial quality control. The RNF41/NRDP1-PRKN pathway regulates autophagosome-lysosome fusion during late mitophagy. May protect RNF41/NRDP1 from proteosomal degradation, RNF41/NRDP1 which regulates proteosomal degradation of PRKN. Plays a key role in beta cells functions by regulating mitophagy/autophagy and mitochondrial health.

Phenotypes From GWAS Catalog for CLEC16A Gene

Gene Ontology (GO) - Molecular Function for CLEC16A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0031267 small GTPase binding IBA --
genes like me logo Genes that share ontologies with CLEC16A: view
genes like me logo Genes that share phenotypes with CLEC16A: view

Animal Models for research

  • Taconic Biosciences Mouse Models for CLEC16A

miRNA for CLEC16A Gene

miRTarBase miRNAs that target CLEC16A

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLEC16A

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CLEC16A Gene

Localization for CLEC16A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLEC16A Gene

Endosome membrane. Peripheral membrane protein. Lysosome membrane. Peripheral membrane protein. Note=Associates with the endolysosome membrane. {ECO:0000250 UniProtKB:Q80U30}.

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 CLEC16A gene
Compartment Confidence
cytosol 5
golgi apparatus 5
endosome 4
lysosome 4
plasma membrane 3
nucleus 3
extracellular 2
mitochondrion 2
cytoskeleton 1
endoplasmic reticulum 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLEC16A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IEA --
GO:0005768 endosome IEA --
GO:0005770 colocalizes_with late endosome IBA 21873635
GO:0005794 Golgi apparatus IDA 28223137
genes like me logo Genes that share ontologies with CLEC16A: view

Pathways & Interactions for CLEC16A Gene

PathCards logo

SuperPathways for CLEC16A Gene

No Data Available

Gene Ontology (GO) - Biological Process for CLEC16A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy IEA --
GO:0008333 endosome to lysosome transport IBA 21873635
GO:0009267 cellular response to starvation IMP 28223137
GO:0016197 endosomal transport IBA 21873635
GO:1901096 regulation of autophagosome maturation IBA 21873635
genes like me logo Genes that share ontologies with CLEC16A: view

No data available for Pathways by source and SIGNOR curated interactions for CLEC16A Gene

Drugs & Compounds for CLEC16A Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for CLEC16A Gene

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  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
  4. Clone products for research

mRNA/cDNA for CLEC16A Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
13 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLEC16A

Alternative Splicing Database (ASD) splice patterns (SP) for CLEC16A Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a · 23b · 23c ^
SP1: - - -
SP2:
SP3:
SP4:
SP5:

ExUns: 24 ^ 25 ^ 26 ^ 27a · 27b
SP1: - -
SP2:
SP3: -
SP4:
SP5:

Relevant External Links for CLEC16A Gene

GeneLoc Exon Structure for
CLEC16A

Expression for CLEC16A Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLEC16A Gene

mRNA expression in normal human tissues for CLEC16A Gene
mRNA expression by BioGPS for CLEC16A GenemRNA expression by GTEx for CLEC16A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)

Protein differential expression in normal tissues from HIPED for CLEC16A Gene

This gene is overexpressed in Cervix (26.8), Islet of Langerhans (18.6), and Peripheral blood mononuclear cells (11.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLEC16A Gene



Protein tissue co-expression partners for CLEC16A Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLEC16A

SOURCE GeneReport for Unigene cluster for CLEC16A Gene:

Hs.35490

mRNA Expression by UniProt/SwissProt for CLEC16A Gene:

Q2KHT3-CL16A_HUMAN
Tissue specificity: Almost exclusively expressed in immune cells, including dendritic cells, B-lymphocytes and natural killer cells.

Evidence on tissue expression from TISSUES for CLEC16A Gene

  • Nervous system(4.8)
  • Pancreas(2.1)
  • Spleen(2.1)
  • Skin(2.1)
  • Blood(2.1)
  • Lymph node(2)
genes like me logo Genes that share expression patterns with CLEC16A: view

Primer products for research

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLEC16A Gene

Orthologs for CLEC16A Gene

This gene was present in the common ancestor of animals.

Orthologs for CLEC16A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia CLEC16A 30 31
  • 99.46 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CLEC16A 30 31
  • 89.62 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CLEC16A 30 31
  • 88.56 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Clec16a 30
  • 87.23 (n)
Mouse
(Mus musculus)
 Mammalia Clec16a 30 17 31
  • 86.98 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia CLEC16A 31
  • 86 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia CLEC16A 31
  • 86 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves CLEC16A 30 31
  • 75.09 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia CLEC16A 31
  • 79 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia clec16a 30
  • 70.12 (n)
Str.6318 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.18966 30
Zebrafish
(Danio rerio)
 Actinopterygii clec16a 30 31
  • 71.49 (n)
 OneToOne
zgc56230 30
Fruit Fly
(Drosophila melanogaster)
 Insecta ema 30 31
  • 58.02 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP002781 30
  • 57.76 (n)
Worm
(Caenorhabditis elegans)
 Secernentea gop-1 30 31
  • 48.87 (n)
 OneToOne
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 55 (a)
 OneToOne
Species where no ortholog for CLEC16A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)

Evolution for CLEC16A Gene

ENSEMBL:
Gene Tree for CLEC16A (if available)
TreeFam:
Gene Tree for CLEC16A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLEC16A: view image

Paralogs for CLEC16A Gene

No data available for Paralogs for CLEC16A Gene

Variants for CLEC16A Gene

Products:

  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLEC16A Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs200082818 Likely Benign: not provided 11,003,289(+) G/A
NM_015226.3(CLEC16A):c.1287G>A (p.Thr429=) 		SYNONYMOUS_VARIANT,INTRON
rs45464291 Benign: not provided 11,003,298(+) G/A
NM_015226.3(CLEC16A):c.1296G>A (p.Glu432=) 		SYNONYMOUS_VARIANT,INTRON
rs61744103 Benign: not provided 11,178,370(+) C/T
NM_015226.3(CLEC16A):c.2842C>T (p.Leu948Phe) 		MISSENSE
rs72650687 Likely Benign: not provided 11,166,421(+) G/A
NM_015226.3(CLEC16A):c.2675G>A (p.Ser892Asn) 		MISSENSE
rs72650689 Likely Benign: not provided 11,178,473(+) G/A
NM_015226.3(CLEC16A):c.2945G>A (p.Ser982Asn) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CLEC16A Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CLEC16A Gene

Variant ID Type Subtype PubMed ID
esv3305974 CNV mobile element insertion 20981092
esv3309233 CNV mobile element insertion 20981092
esv3375909 CNV duplication 20981092
esv3637921 CNV gain 21293372
nsv103022 CNV deletion 16902084
nsv1037733 CNV loss 25217958
nsv1040428 CNV gain 25217958
nsv1043915 CNV loss 25217958
nsv525548 CNV loss 19592680
nsv952919 CNV deletion 24416366
nsv952920 CNV deletion 24416366
nsv977903 CNV duplication 23825009

Variation tolerance for CLEC16A Gene

Residual Variation Intolerance Score: 63.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.41; 54.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLEC16A Gene

Human Gene Mutation Database (HGMD)
CLEC16A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLEC16A

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLEC16A Gene

Disorders for CLEC16A Gene

MalaCards: The human disease database

(10) MalaCards diseases for CLEC16A Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CL16A_HUMAN
  • Diabetes mellitus, insulin-dependent (IDDM) [MIM:222100]: A multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical features are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269 PubMed:17632545, ECO:0000269 PubMed:24949970}. Note=Disease susceptibility is associated with variants affecting the gene represented in this entry. Three common non-coding variants of CLEC16A in strong linkage disequilibrium reach genome-wide significance for association with the disease (PubMed:17632545). The non-coding variant rs12708716 is associated with reduced expression of CLEC16A in beta cells and reduced beta cell function (PubMed:24949970). {ECO:0000269 PubMed:17632545, ECO:0000269 PubMed:24949970}.

Additional Disease Information for CLEC16A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CLEC16A: view

No data available for Genatlas for CLEC16A Gene

Publications for CLEC16A Gene

  1. A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene. (PMID: 17632545) Hakonarson H … Polychronakos C (Nature 2007) 2 3 4 41
  2. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9205841) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4
  3. The diabetes susceptibility gene Clec16a regulates mitophagy. (PMID: 24949970) Soleimanpour SA … Stoffers DA (Cell 2014) 3 4
  4. A genome-wide meta-analysis of genetic variants associated with allergic rhinitis and grass sensitization and their interaction with birth order. (PMID: 22036096) Ramasamy A … Jarvis DL (The Journal of allergy and clinical immunology 2011) 3 41
  5. Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases. (PMID: 21829393) Plagnol V … Todd JA (PLoS genetics 2011) 3 41

ExternalLinks

View latest publications for CLEC16A gene in Mastermind

Products for CLEC16A Gene

Sources for CLEC16A Gene