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

    Gene ID: 23274, updated on 9-Dec-2024

    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
    Try the new Transcript table

    Genomic context

    See CLEC16A in Genome Data Viewer
    Location:
    16p13.13
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (10944564..11182186)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (10980535..11218466)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (11038421..11276043)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10391 Neighboring gene Rho GTPase activating protein 21 pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:10964767-10965966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10399 Neighboring gene class II major histocompatibility complex transactivator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10401 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10406 Neighboring gene Sharpr-MPRA regulatory region 12638 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11066007-11066184 Neighboring gene Dexi homolog Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11073759-11074260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11074261-11074760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7196 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11099817-11100053 Neighboring gene NANOG hESC enhancer GRCh37_chr16:11101530-11102234 Neighboring gene Sharpr-MPRA regulatory region 10204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11144189-11144765 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11144766-11145343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10407 Neighboring gene ribosomal protein L7 pseudogene 46 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10412 Neighboring gene Sharpr-MPRA regulatory region 12604 Neighboring gene uncharacterized LOC105371081 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11234005-11234583 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11234584-11235161 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11235162-11235740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11238795-11239462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11268031-11268544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11275481-11276366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11276367-11277253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11290798-11291307 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11291308-11291816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11292853-11293353 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:11295121-11296320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11296313-11297109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11304646-11305240 Neighboring gene uncharacterized LOC107984859 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10424 Neighboring gene CRISPRi-validated cis-regulatory element chr16.1224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10425 Neighboring gene Sharpr-MPRA regulatory region 4189 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 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

    Clone Names

    • KIAA0350, MGC111457

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    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
     
    involved_in mitophagy IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of autophagosome maturation 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
     
    involved_in vacuolar transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with late endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
     
    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
      UniProtKB/TrEMBL
      A0A8V8TR67
      Related
      ENSP00000515187.1, ENST00000703130.1
    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
      O15058, Q2KHT3, Q6ZTB2
      Related
      ENSP00000387122.1, ENST00000409790.6
      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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 X5

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    2. XM_011522434.3XP_011520736.1  protein CLEC16A isoform X3

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    3. XM_005255211.3XP_005255268.1  protein CLEC16A isoform X1

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    4. XM_047433851.1XP_047289807.1  protein CLEC16A isoform X8

    5. XM_047433848.1XP_047289804.1  protein CLEC16A isoform X6

    6. XM_047433847.1XP_047289803.1  protein CLEC16A isoform X4

    7. XM_005255213.3XP_005255270.1  protein CLEC16A isoform X2

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    8. XM_047433852.1XP_047289808.1  protein CLEC16A isoform X9

    9. XM_047433850.1XP_047289806.1  protein CLEC16A isoform X7

    10. XM_047433853.1XP_047289809.1  protein CLEC16A isoform X10

    11. XM_047433855.1XP_047289811.1  protein CLEC16A isoform X14

    12. XM_047433854.1XP_047289810.1  protein CLEC16A isoform X11

    13. XM_047433856.1XP_047289812.1  protein CLEC16A isoform X15

    14. XM_005255215.5XP_005255272.1  protein CLEC16A isoform X17

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    15. XM_005255216.3XP_005255273.1  protein CLEC16A isoform X24

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    16. XM_024450218.2XP_024305986.1  protein CLEC16A isoform X18

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; Uncharacterized conserved protein
    17. XM_047433860.1XP_047289816.1  protein CLEC16A isoform X25

    18. XM_047433866.1XP_047289822.1  protein CLEC16A isoform X31

    19. XM_011522438.4XP_011520740.1  protein CLEC16A isoform X19

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    20. XM_047433861.1XP_047289817.1  protein CLEC16A isoform X26

    21. XM_047433858.1XP_047289814.1  protein CLEC16A isoform X20

    22. XM_047433867.1XP_047289823.1  protein CLEC16A isoform X32

    23. XM_047433862.1XP_047289818.1  protein CLEC16A isoform X27

    24. XM_011522436.4XP_011520738.1  protein CLEC16A isoform X12

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    25. XM_011522437.4XP_011520739.1  protein CLEC16A isoform X13

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    26. XM_011522439.4XP_011520741.1  protein CLEC16A isoform X21

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    27. XM_011522440.4XP_011520742.1  protein CLEC16A isoform X22

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    28. XM_047433863.1XP_047289819.1  protein CLEC16A isoform X28

    29. XM_047433859.1XP_047289815.1  protein CLEC16A isoform X23

    30. XM_047433857.1XP_047289813.1  protein CLEC16A isoform X16

    31. XM_047433864.1XP_047289820.1  protein CLEC16A isoform X29

    32. XM_047433865.1XP_047289821.1  protein CLEC16A isoform X30

    33. XM_006720870.5XP_006720933.1  protein CLEC16A isoform X33

      Conserved Domains (1) summary
      pfam09758
      Location:51198
      FPL; uncharacterized conserved protein
    34. XM_047433868.1XP_047289824.1  protein CLEC16A isoform X34

    35. XM_017023089.3XP_016878578.1  protein CLEC16A isoform X35

    36. XM_024450219.2XP_024305987.1  protein CLEC16A isoform X36

    37. XM_017023090.3XP_016878579.1  protein CLEC16A isoform X37

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

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

    mRNA and Protein(s)

    1. XM_054379921.1XP_054235896.1  protein CLEC16A isoform X5

    2. XM_054379919.1XP_054235894.1  protein CLEC16A isoform X3

    3. XM_054379917.1XP_054235892.1  protein CLEC16A isoform X1

    4. XM_054379924.1XP_054235899.1  protein CLEC16A isoform X8

    5. XM_054379922.1XP_054235897.1  protein CLEC16A isoform X6

    6. XM_054379920.1XP_054235895.1  protein CLEC16A isoform X4

    7. XM_054379918.1XP_054235893.1  protein CLEC16A isoform X2

    8. XM_054379925.1XP_054235900.1  protein CLEC16A isoform X9

    9. XM_054379923.1XP_054235898.1  protein CLEC16A isoform X7

    10. XM_054379926.1XP_054235901.1  protein CLEC16A isoform X10

    11. XM_054379930.1XP_054235905.1  protein CLEC16A isoform X14

    12. XM_054379927.1XP_054235902.1  protein CLEC16A isoform X11

    13. XM_054379931.1XP_054235906.1  protein CLEC16A isoform X15

    14. XM_054379933.1XP_054235908.1  protein CLEC16A isoform X17

    15. XM_054379940.1XP_054235915.1  protein CLEC16A isoform X24

    16. XM_054379934.1XP_054235909.1  protein CLEC16A isoform X18

    17. XM_054379941.1XP_054235916.1  protein CLEC16A isoform X25

    18. XM_054379947.1XP_054235922.1  protein CLEC16A isoform X31

    19. XM_054379935.1XP_054235910.1  protein CLEC16A isoform X19

    20. XM_054379942.1XP_054235917.1  protein CLEC16A isoform X26

    21. XM_054379936.1XP_054235911.1  protein CLEC16A isoform X20

    22. XM_054379948.1XP_054235923.1  protein CLEC16A isoform X32

    23. XM_054379943.1XP_054235918.1  protein CLEC16A isoform X27

    24. XM_054379928.1XP_054235903.1  protein CLEC16A isoform X12

    25. XM_054379929.1XP_054235904.1  protein CLEC16A isoform X13

    26. XM_054379937.1XP_054235912.1  protein CLEC16A isoform X21

    27. XM_054379938.1XP_054235913.1  protein CLEC16A isoform X22

    28. XM_054379944.1XP_054235919.1  protein CLEC16A isoform X28

    29. XM_054379939.1XP_054235914.1  protein CLEC16A isoform X23

    30. XM_054379932.1XP_054235907.1  protein CLEC16A isoform X16

    31. XM_054379945.1XP_054235920.1  protein CLEC16A isoform X29

    32. XM_054379946.1XP_054235921.1  protein CLEC16A isoform X30

    33. XM_054379949.1XP_054235924.1  protein CLEC16A isoform X33

    34. XM_054379950.1XP_054235925.1  protein CLEC16A isoform X34

    35. XM_054379951.1XP_054235926.1  protein CLEC16A isoform X35

    36. XM_054379952.1XP_054235927.1  protein CLEC16A isoform X36

    37. XM_054379953.1XP_054235928.1  protein CLEC16A isoform X37