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CLEC16A C-type lectin domain containing 16A [ Homo sapiens (human) ]

Gene ID: 23274, updated on 4-Nov-2018

Summary

Official Symbol
CLEC16Aprovided by HGNC
Official Full Name
C-type lectin domain containing 16Aprovided by HGNC
Primary source
HGNC:HGNC:29013
See related
Ensembl:ENSG00000038532 MIM:611303; Vega:OTTHUMG00000152915
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Gop-1; KIAA0350
Summary
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]
Expression
Broad expression in testis (RPKM 11.3), brain (RPKM 3.5) and 24 other tissues See more
Orthologs

Genomic context

See CLEC16A in Genome Data Viewer
Location:
16p13.13
Exon count:
35
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (10944488..11193272)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (11038345..11276046)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112267907 Neighboring gene class II major histocompatibility complex transactivator Neighboring gene Dexi homolog Neighboring gene ribosomal protein L7 pseudogene 46 Neighboring gene uncharacterized LOC105371081 Neighboring gene uncharacterized LOC107984859 Neighboring gene heterogeneous nuclear ribonucleoprotein C pseudogene 4

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.
NHGRI GWA Catalog
A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene.
NHGRI GWA Catalog
A genome-wide meta-analysis of genetic variants associated with allergic rhinitis and grass sensitization and their interaction with birth order.
NHGRI GWA Catalog
Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency.
NHGRI GWA Catalog
Common variants at ten loci influence QT interval duration in the QTGEN Study.
NHGRI GWA Catalog
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
NHGRI GWA Catalog
Genome-wide association analysis identifies 11 risk variants associated with the asthma with hay fever phenotype.
NHGRI GWA Catalog
Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.
NHGRI GWA Catalog
Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
NHGRI GWA Catalog
Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.
NHGRI GWA Catalog
Genome-wide association study identifies eight new susceptibility loci for atopic dermatitis in the Japanese population.
NHGRI GWA Catalog
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
NHGRI GWA Catalog
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
NHGRI GWA Catalog
Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci.
NHGRI GWA Catalog
Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci.
NHGRI GWA Catalog
Multiple common variants for celiac disease influencing immune gene expression.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog
Risk alleles for multiple sclerosis identified by a genomewide study.
NHGRI GWA Catalog
Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0350, MGC111457

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab GTPase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
molecular_function ND
No biological Data available
more info
 
Process Evidence Code Pubs
autophagy IEA
Inferred from Electronic Annotation
more info
 
cellular response to starvation IMP
Inferred from Mutant Phenotype
more info
PubMed 
endosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome to lysosome transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of autophagosome maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of macroautophagy by TORC1 signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of mitophagy IEA
Inferred from Electronic Annotation
more info
 
negative regulation of proteasomal ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of TORC1 signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of autophagosome maturation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
endolysosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
colocalizes_with late endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
vesicle IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
protein CLEC16A
Names
C-type lectin domain family 16 member A

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_016757.1 RefSeqGene

    Range
    5001..242702
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243403.1NP_001230332.1  protein CLEC16A isoform 2

    See identical proteins and their annotated locations for NP_001230332.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, uses an alternate in-frame splice site and differs in the 3' coding region and UTR compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BC112897, BX374760, DB062118, DB069341
    Consensus CDS
    CCDS58423.1
    UniProtKB/Swiss-Prot
    Q2KHT3
    Related
    ENSP00000386495.3, OTTHUMP00000202698, ENST00000409552.4, OTTHUMT00000328542
    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  2. NM_015226.2NP_056041.1  protein CLEC16A isoform 1

    See identical proteins and their annotated locations for NP_056041.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
    Source sequence(s)
    AB002348, AW072095, DB069341
    Consensus CDS
    CCDS45409.1
    UniProtKB/Swiss-Prot
    Q2KHT3
    Related
    ENSP00000387122.1, OTTHUMP00000202696, ENST00000409790.5, OTTHUMT00000328540
    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

    Range
    10944488..11193272
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522435.2XP_011520737.1  protein CLEC16A isoform X6

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  2. XM_005255214.2XP_005255271.1  protein CLEC16A isoform X5

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  3. XM_011522434.2XP_011520736.1  protein CLEC16A isoform X4

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  4. XM_005255211.2XP_005255268.1  protein CLEC16A isoform X2

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  5. XM_005255210.2XP_005255267.1  protein CLEC16A isoform X1

    See identical proteins and their annotated locations for XP_005255267.1

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  6. XM_005255213.2XP_005255270.1  protein CLEC16A isoform X3

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  7. XM_005255215.4XP_005255272.1  protein CLEC16A isoform X9

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  8. XM_005255216.2XP_005255273.1  protein CLEC16A isoform X14

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  9. XM_024450218.1XP_024305986.1  protein CLEC16A isoform X10

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; Uncharacterized conserved protein
  10. XM_011522438.3XP_011520740.1  protein CLEC16A isoform X11

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  11. XM_011522436.3XP_011520738.1  protein CLEC16A isoform X7

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  12. XM_011522437.3XP_011520739.1  protein CLEC16A isoform X8

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  13. XM_011522439.3XP_011520741.1  protein CLEC16A isoform X12

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  14. XM_011522440.3XP_011520742.1  protein CLEC16A isoform X13

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  15. XM_006720870.4XP_006720933.1  protein CLEC16A isoform X15

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  16. XM_017023089.2XP_016878578.1  protein CLEC16A isoform X16

  17. XM_024450219.1XP_024305987.1  protein CLEC16A isoform X17

  18. XM_017023090.2XP_016878579.1  protein CLEC16A isoform X18

RNA

  1. XR_932810.3 RNA Sequence

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