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

Gene ID: 23274, updated on 26-Oct-2022

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; AllianceGenome:HGNC:29013
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
NEW
Try the new Gene table
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Genomic context

See CLEC16A in Genome Data Viewer
Location:
16p13.13
Exon count:
33
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (10944564..11182186)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (10980535..11218466)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (11038421..11276043)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene Rho GTPase activating protein 21 pseudogene Neighboring gene class II major histocompatibility complex transactivator Neighboring gene Dexi homolog Neighboring gene ribosomal protein L7 pseudogene 46 Neighboring gene Sharpr-MPRA regulatory region 12604 Neighboring gene uncharacterized LOC105371081 Neighboring gene uncharacterized LOC107984859 Neighboring gene CRISPRi-validated cis-regulatory element chr16.1224

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Pathways from PubChem

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
enables molecular_function ND
No biological Data available
more info
 
Process Evidence Code Pubs
involved_in autophagy IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to starvation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in endosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in endosome to lysosome transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of autophagosome maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of macroautophagy by TORC1 signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of TORC1 signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of autophagosome maturation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in endolysosome 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 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in 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)

NEW Try the new Transcript table

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
    5077..242699
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243403.2NP_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, ENST00000409552.4
    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  2. NM_001410905.1NP_001397834.1  protein CLEC16A isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC007014, AC007220, AC133065
    Consensus CDS
    CCDS92106.1
  3. NM_015226.3NP_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, Q6ZTB2
    Related
    ENSP00000387122.1, ENST00000409790.6
    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    10944564..11182186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005255214.3XP_005255271.1  protein CLEC16A isoform X6

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

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  3. XM_005255211.3XP_005255268.1  protein CLEC16A isoform X2

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  4. XM_047433851.1XP_047289807.1  protein CLEC16A isoform X9

  5. XM_005255210.3XP_005255267.1  protein CLEC16A isoform X1

    Related
    ENSP00000515187.1, ENST00000703130.1
    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  6. XM_047433848.1XP_047289804.1  protein CLEC16A isoform X7

  7. XM_047433847.1XP_047289803.1  protein CLEC16A isoform X5

  8. XM_005255213.3XP_005255270.1  protein CLEC16A isoform X3

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  9. XM_047433852.1XP_047289808.1  protein CLEC16A isoform X10

  10. XM_047433850.1XP_047289806.1  protein CLEC16A isoform X8

  11. XM_047433853.1XP_047289809.1  protein CLEC16A isoform X11

  12. XM_047433855.1XP_047289811.1  protein CLEC16A isoform X15

  13. XM_047433854.1XP_047289810.1  protein CLEC16A isoform X12

  14. XM_047433856.1XP_047289812.1  protein CLEC16A isoform X16

  15. XM_005255215.5XP_005255272.1  protein CLEC16A isoform X18

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  16. XM_005255216.3XP_005255273.1  protein CLEC16A isoform X25

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  17. XM_024450218.2XP_024305986.1  protein CLEC16A isoform X19

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; Uncharacterized conserved protein
  18. XM_047433860.1XP_047289816.1  protein CLEC16A isoform X26

  19. XM_047433866.1XP_047289822.1  protein CLEC16A isoform X32

  20. XM_011522438.4XP_011520740.1  protein CLEC16A isoform X20

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  21. XM_047433861.1XP_047289817.1  protein CLEC16A isoform X27

  22. XM_047433858.1XP_047289814.1  protein CLEC16A isoform X21

  23. XM_047433867.1XP_047289823.1  protein CLEC16A isoform X33

  24. XM_047433862.1XP_047289818.1  protein CLEC16A isoform X28

  25. XM_011522436.4XP_011520738.1  protein CLEC16A isoform X13

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  26. XM_011522437.4XP_011520739.1  protein CLEC16A isoform X14

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  27. XM_011522439.4XP_011520741.1  protein CLEC16A isoform X22

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  28. XM_011522440.4XP_011520742.1  protein CLEC16A isoform X23

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  29. XM_047433863.1XP_047289819.1  protein CLEC16A isoform X29

  30. XM_047433859.1XP_047289815.1  protein CLEC16A isoform X24

  31. XM_047433857.1XP_047289813.1  protein CLEC16A isoform X17

  32. XM_047433864.1XP_047289820.1  protein CLEC16A isoform X30

  33. XM_047433865.1XP_047289821.1  protein CLEC16A isoform X31

  34. XM_006720870.5XP_006720933.1  protein CLEC16A isoform X34

    Conserved Domains (1) summary
    pfam09758
    Location:51198
    FPL; uncharacterized conserved protein
  35. XM_047433868.1XP_047289824.1  protein CLEC16A isoform X35

  36. XM_017023089.3XP_016878578.1  protein CLEC16A isoform X36

  37. XM_024450219.2XP_024305987.1  protein CLEC16A isoform X37

  38. XM_017023090.3XP_016878579.1  protein CLEC16A isoform X38

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    10980535..11218466
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)