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    ATG16L2 autophagy related 16 like 2 [ Homo sapiens (human) ]

    Gene ID: 89849, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ATG16L2provided by HGNC
    Official Full Name
    autophagy related 16 like 2provided by HGNC
    Primary source
    HGNC:HGNC:25464
    See related
    Ensembl:ENSG00000168010 MIM:618716; AllianceGenome:HGNC:25464
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    WDR80; ATG16B
    Summary
    Predicted to be involved in autophagosome assembly. Predicted to act upstream of or within negative stranded viral RNA replication. Located in nucleoplasm. Part of Atg12-Atg5-Atg16 complex. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in spleen (RPKM 22.5), skin (RPKM 19.9) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATG16L2 in Genome Data Viewer
    Location:
    11q13.4
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (72814411..72843740)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (72742639..72773369)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (72525456..72540680)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene StAR related lipid transfer domain containing 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:72497138-72498136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:72498137-72499133 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:72503217-72503716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5206 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:72509227-72509964 Neighboring gene uncharacterized LOC107984421 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3729 Neighboring gene microRNA 4692 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3731 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5209 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5210 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:72537383-72537883 Neighboring gene NANOG hESC enhancer GRCh37_chr11:72559943-72560444 Neighboring gene FCH and double SH3 domains 2 Neighboring gene RNA, U6 small nuclear 672, pseudogene Neighboring gene Sharpr-MPRA regulatory region 15519 Neighboring gene ribosomal protein L15 pseudogene 16

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. The role of ATG16L2 in autophagy and disease. Don Wai Luu L, et al. Autophagy, 2022 Nov. PMID 35239457, Free PMC Article
    2. Identification of a novel differentially methylated region adjacent to ATG16L2 in lung cancer cells using methyl-CpG binding domain protein-enriched genome sequencing. Bai H, et al. Genome, 2021 May. PMID 33113339
    3. Potentially Functional Variants of ATG16L2 Predict Radiation Pneumonitis and Outcomes in Patients with Non-Small Cell Lung Cancer after Definitive Radiotherapy. Wen J, et al. J Thorac Oncol, 2018 May. PMID 29454863, Free PMC Article
    4. A functional variant of ATG16L2 is associated with Crohn's disease in the Chinese population. Ma T, et al. Colorectal Dis, 2016 Nov. PMID 27611316
    5. Autophagy-related gene16L2, a potential serum biomarker of multiple sclerosis evaluated by bead-based proteomic technology. Yin L, et al. Neurosci Lett, 2014 Mar 6. PMID 24406150

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The role of ATG16L2 in autophagy and disease.
      Title: The role of ATG16L2 in autophagy and disease.
    2. Identification of a novel differentially methylated region adjacent to ATG16L2 in lung cancer cells using methyl-CpG binding domain protein-enriched genome sequencing.
      Title: Identification of a novel differentially methylated region adjacent to ATG16L2 in lung cancer cells using methyl-CpG binding domain protein-enriched genome sequencing.
    3. Results found ATG16L2 rs10898880 was significantly associated with the occurrence of grade 3-4 oral mucositis and myelosuppression in nasopharyngeal carcinoma (NPC) patients treated with radiotherapy.
      Title: Potentially functional variants of autophagy-related genes are associated with the efficacy and toxicity of radiotherapy in patients with nasopharyngeal carcinoma.
    4. Patients with the ATG16L2 rs10898880 CC variant genotype had a better LRFS, PFS, and OS (adjusted hazard ratio = 0.59, 0.64, and 0.64; 95% confidence interval: 0.45-0.79, 0.48-0.84, and 0.48-0.86; p = 0.0004, 0.002, and 0.003, respectively), but a greater risk for development of severe RP (adjusted hazard ratio = 1.80, 95% confidence interval: 1.04-3.12, p = 0.037) than did patients with AA/AC genotypes.
      Title: Potentially Functional Variants of ATG16L2 Predict Radiation Pneumonitis and Outcomes in Patients with Non-Small Cell Lung Cancer after Definitive Radiotherapy.
    5. ATG16L2 is a susceptibility gene for Crohn's disease in the Chinese population. The rs11235604 single nucleotide polymorphism is remarkably associated with downregulation of the expression of ATG16L2.
      Title: A functional variant of ATG16L2 is associated with Crohn's disease in the Chinese population.
    6. A novel SNP-systemic lupus erythematosus association was identified between FCHSD2 and P2RY2, peaking at rs11235667 on a 33-kb haplotype upstream of ATG16L2.
      Title: Identification of a Systemic Lupus Erythematosus Risk Locus Spanning ATG16L2, FCHSD2, and P2RY2 in Koreans.
    7. Atg16L2 may play an important role in autophagy of T cells and serve as a potential biomarker to predict clinical relapse of Multiple sclerosis
      Title: Autophagy-related gene16L2, a potential serum biomarker of multiple sclerosis evaluated by bead-based proteomic technology.
    8. Three novel risk loci including ATG16L2 were discovered by genome-wide association study in the Korean Crohn's disease population, of which two showed patterns of association in the International Inflammatory Bowel Disease Genetics Consortium dataset.
      Title: Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population.
    EBI GWAS Catalog
    Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    High levels of additive and synergic antiretroviral activity are obtained by using antiretroviral compounds (T1249, 3TC, RAL, or IDV) in PM1 cells stably expressing anti-host shRNAs (IPO7, HSPD1, or ATG16) or anti-HIV shRNAs (Pol, RT, or Nef) PubMed
    Knockdown of ATG16 autophagy related 16-like 2 (ATG16L2) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef High levels of additive and synergic antiretroviral activity are obtained by using antiretroviral compounds (T1249, 3TC, RAL, or IDV) in PM1 cells stably expressing anti-host shRNAs (IPO7, HSPD1, or ATG16) or anti-HIV shRNAs (Pol, RT, or Nef) PubMed
    Pol gag-pol High levels of additive and synergic antiretroviral activity are obtained by using antiretroviral compounds (T1249, 3TC, RAL, or IDV) in PM1 cells stably expressing anti-host shRNAs (IPO7, HSPD1, or ATG16) or anti-HIV shRNAs (Pol, RT, or Nef) PubMed
    reverse transcriptase gag-pol High levels of additive and synergic antiretroviral activity are obtained by using antiretroviral compounds (T1249, 3TC, RAL, or IDV) in PM1 cells stably expressing anti-host shRNAs (IPO7, HSPD1, or ATG16) or anti-HIV shRNAs (Pol, RT, or Nef) PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ00012

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT involved_in autophagosome assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    NOT involved_in autophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in macroautophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative stranded viral RNA replication IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Atg12-Atg5-Atg16 complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    NOT located_in autophagosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in phagophore assembly site membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    protein Atg16l2
    Names
    APG16-like 2
    ATG16 autophagy related 16-like 2
    WD repeat-containing protein 80
    autophagy-related protein 16-2

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001318766.2 → NP_001305695.1  protein Atg16l2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AK090597, AL832974, AP002381, BC137489
      UniProtKB/Swiss-Prot
      Q8NAA4
      Conserved Domains (4) summary
      COG2319
      Location:218 → 513
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:225 → 513
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam14971
      Location:18 → 98
      DUF4510; Domain of unknown function (DUF4510)
      sd00039
      Location:235 → 272
      7WD40; WD40 repeat [structural motif]

    2. NM_033388.2 → NP_203746.1  protein Atg16l2 isoform 1

      See identical proteins and their annotated locations for NP_203746.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK024423, AK090597, AL832974, BC036713, BC069189, BQ929430
      Consensus CDS
      CCDS31634.1
      UniProtKB/Swiss-Prot
      A5PL30, B2RPK5, Q658V4, Q6PID3, Q8NAA4, Q8NBG0
      Related
      ENSP00000326340.5, ENST00000321297.10
      Conserved Domains (5) summary
      COG2319
      Location:324 → 619
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:331 → 619
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam02050
      Location:86 → 190
      FliJ; Flagellar FliJ protein
      pfam08614
      Location:17 → 203
      ATG16; Autophagy protein 16 (ATG16)
      sd00039
      Location:341 → 378
      7WD40; WD40 repeat [structural motif]

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      72814411..72843740
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005274376.6 → XP_005274433.1  protein Atg16l2 isoform X1

      Conserved Domains (5) summary
      COG2319
      Location:324 → 586
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:331 → 588
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam02050
      Location:86 → 190
      FliJ; Flagellar FliJ protein
      pfam08614
      Location:17 → 203
      ATG16; Autophagy protein 16 (ATG16)
      sd00039
      Location:341 → 378
      7WD40; WD40 repeat [structural motif]

    2. XM_047427840.1 → XP_047283796.1  protein Atg16l2 isoform X4

    3. XM_006718732.3 → XP_006718795.1  protein Atg16l2 isoform X2

      Conserved Domains (5) summary
      COG2319
      Location:303 → 598
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:310 → 598
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam02050
      Location:86 → 190
      FliJ; Flagellar FliJ protein
      pfam08614
      Location:17 → 203
      ATG16; Autophagy protein 16 (ATG16)
      sd00039
      Location:320 → 357
      7WD40; WD40 repeat [structural motif]

    4. XM_011545332.2 → XP_011543634.1  protein Atg16l2 isoform X3

      Conserved Domains (5) summary
      COG2319
      Location:286 → 581
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:293 → 581
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam02050
      Location:86 → 190
      FliJ; Flagellar FliJ protein
      pfam08614
      Location:17 → 203
      ATG16; Autophagy protein 16 (ATG16)
      sd00039
      Location:303 → 340
      7WD40; WD40 repeat [structural motif]

    5. XM_047427841.1 → XP_047283797.1  protein Atg16l2 isoform X6

    6. XM_006718733.4 → XP_006718796.1  protein Atg16l2 isoform X7

      Conserved Domains (1) summary
      pfam08614
      Location:17 → 203
      ATG16; Autophagy protein 16 (ATG16)

    7. XM_011545334.2 → XP_011543636.1  protein Atg16l2 isoform X5

      See identical proteins and their annotated locations for XP_011543636.1

      UniProtKB/Swiss-Prot
      Q8NAA4
      Conserved Domains (4) summary
      COG2319
      Location:218 → 513
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:225 → 513
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam14971
      Location:18 → 98
      DUF4510; Domain of unknown function (DUF4510)
      sd00039
      Location:235 → 272
      7WD40; WD40 repeat [structural motif]

    8. XM_011545333.2 → XP_011543635.1  protein Atg16l2 isoform X5

      See identical proteins and their annotated locations for XP_011543635.1

      UniProtKB/Swiss-Prot
      Q8NAA4
      Conserved Domains (4) summary
      COG2319
      Location:218 → 513
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:225 → 513
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      pfam14971
      Location:18 → 98
      DUF4510; Domain of unknown function (DUF4510)
      sd00039
      Location:235 → 272
      7WD40; WD40 repeat [structural motif]

    9. XM_047427842.1 → XP_047283798.1  protein Atg16l2 isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      72742639..72773369
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370416.1 → XP_054226391.1  protein Atg16l2 isoform X1

    2. XM_054370419.1 → XP_054226394.1  protein Atg16l2 isoform X4

    3. XM_054370417.1 → XP_054226392.1  protein Atg16l2 isoform X2

    4. XM_054370418.1 → XP_054226393.1  protein Atg16l2 isoform X3

    5. XM_054370421.1 → XP_054226396.1  protein Atg16l2 isoform X6

    6. XM_054370423.1 → XP_054226398.1  protein Atg16l2 isoform X7

    7. XM_054370422.1 → XP_054226397.1  protein Atg16l2 isoform X5

    8. XM_054370420.1 → XP_054226395.1  protein Atg16l2 isoform X5

    9. XM_054370424.1 → XP_054226399.1  protein Atg16l2 isoform X8

    10. XM_054370425.1 → XP_054226400.1  protein Atg16l2 isoform X8

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NAA4.2 GenPept UniProtKB/Swiss-Prot:Q8NAA4

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