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ATG16L1 autophagy related 16 like 1 [ Homo sapiens (human) ]

Gene ID: 55054, updated on 17-May-2020

Summary

Official Symbol
ATG16L1provided by HGNC
Official Full Name
autophagy related 16 like 1provided by HGNC
Primary source
HGNC:HGNC:21498
See related
Ensembl:ENSG00000085978 MIM:610767
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
IBD10; WDR30; APG16L; ATG16A; ATG16L
Summary
The protein encoded by this gene is part of a large protein complex that is necessary for autophagy, the major process by which intracellular components are targeted to lysosomes for degradation. Defects in this gene are a cause of susceptibility to inflammatory bowel disease type 10 (IBD10). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jun 2010]
Expression
Ubiquitous expression in bone marrow (RPKM 12.7), testis (RPKM 12.0) and 25 other tissues See more
Orthologs

Genomic context

See ATG16L1 in Genome Data Viewer
Location:
2q37.1
Exon count:
19
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (233251571..233295674)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (234160217..234204320)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene neuraminidase 2 Neighboring gene inositol polyphosphate-5-phosphatase D Neighboring gene RNA, 7SL, cytoplasmic 32, pseudogene Neighboring gene small Cajal body-specific RNA 5 Neighboring gene small Cajal body-specific RNA 6 Neighboring gene S-antigen visual arrestin Neighboring gene diacylglycerol kinase delta Neighboring gene Sharpr-MPRA regulatory region 11245

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

Associated conditions

Description Tests
Inflammatory bowel disease 10
MedGen: C1970207 OMIM: 611081 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300.
NHGRI GWA Catalog
A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
NHGRI GWA Catalog
Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease.
NHGRI GWA Catalog
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
NHGRI GWA Catalog
Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis.
NHGRI GWA Catalog
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
NHGRI GWA Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog

HIV-1 interactions

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

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ00045, FLJ10035, FLJ10828, FLJ22677

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin-like protein transferase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
autophagosome assembly NAS
Non-traceable Author Statement
more info
PubMed 
macroautophagy TAS
Traceable Author Statement
more info
 
negative stranded viral RNA replication IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
autophagosome ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
autophagosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axoneme ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol TAS
Traceable Author Statement
more info
 
phagophore assembly site membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
autophagy-related protein 16-1
Names
APG16L beta
ATG16 autophagy related 16-like 1
WD repeat domain 30

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_023038.1 RefSeqGene

    Range
    5103..49099
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001190266.2NP_001177195.1  autophagy-related protein 16-1 isoform 4

    See identical proteins and their annotated locations for NP_001177195.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice junction at the 3' end of a coding exon compared to variant 1, that causes a frameshift. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC013726, BC000061, BC071846, DB084962
    UniProtKB/Swiss-Prot
    Q676U5
    UniProtKB/TrEMBL
    Q53SV2
    Conserved Domains (3) summary
    cd00200
    Location:231521
    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 ...
    sd00039
    Location:243280
    7WD40; WD40 repeat [structural motif]
    pfam08614
    Location:2122
    ATG16; Autophagy protein 16 (ATG16)
  2. NM_001190267.2NP_001177196.1  autophagy-related protein 16-1 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice junction at the 5' end of a coding exon compared to variant 1, that causes a frameshift. The resulting isoform (5) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC013726, BC000061, BC006253, BC071846, DB084962
    UniProtKB/Swiss-Prot
    Q676U5
    Conserved Domains (4) summary
    COG2319
    Location:199457
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:199489
    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 ...
    sd00039
    Location:211248
    7WD40; WD40 repeat [structural motif]
    cl23720
    Location:1110
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
  3. NM_001363742.2NP_001350671.1  autophagy-related protein 16-1 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has an additional in-frame exon compared to variant 1. The resulting isoform (6) has the same N- and C-termini but is longer compared to isoform 1.
    Source sequence(s)
    AC013726
    Consensus CDS
    CCDS86927.1
    Related
    ENSP00000375873.1, ENST00000392018.1
    Conserved Domains (4) summary
    COG2319
    Location:272390
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:332622
    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 ...
    sd00039
    Location:344381
    7WD40; WD40 repeat [structural motif]
    pfam08614
    Location:31206
    ATG16; Autophagy protein 16 (ATG16)
  4. NM_017974.4NP_060444.3  autophagy-related protein 16-1 isoform 2

    See identical proteins and their annotated locations for NP_060444.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AA809053, AC013726, AK001690, BC117337, DB084962, DB474638
    Consensus CDS
    CCDS2502.2
    UniProtKB/Swiss-Prot
    Q676U5
    UniProtKB/TrEMBL
    A0A024R494, Q17RG0
    Related
    ENSP00000375875.4, ENST00000392020.8
    Conserved Domains (5) summary
    COG2319
    Location:296554
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:296586
    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 ...
    pfam08614
    Location:31206
    ATG16; Autophagy protein 16 (ATG16)
    sd00039
    Location:308345
    7WD40; WD40 repeat [structural motif]
    cl23720
    Location:117222
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
  5. NM_030803.7NP_110430.5  autophagy-related protein 16-1 isoform 1

    See identical proteins and their annotated locations for NP_110430.5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AA809053, AC013726, AY398617, BC117337, DB084962
    Consensus CDS
    CCDS2503.2
    UniProtKB/Swiss-Prot
    Q676U5
    UniProtKB/TrEMBL
    Q17RG0
    Related
    ENSP00000375872.4, ENST00000392017.9
    Conserved Domains (5) summary
    COG2319
    Location:315573
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:315605
    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 ...
    pfam08614
    Location:31206
    ATG16; Autophagy protein 16 (ATG16)
    sd00039
    Location:327364
    7WD40; WD40 repeat [structural motif]
    cl23720
    Location:117222
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
  6. NM_198890.2NP_942593.2  autophagy-related protein 16-1 isoform 3

    See identical proteins and their annotated locations for NP_942593.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame segment and an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AA809053, AC013726, BC071846, DB084962, EF079890
    Consensus CDS
    CCDS54438.1
    UniProtKB/Swiss-Prot
    Q676U5
    Related
    ENSP00000318259.6, ENST00000347464.9
    Conserved Domains (3) summary
    COG2319
    Location:152410
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:152442
    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 ...
    sd00039
    Location:164201
    7WD40; WD40 repeat [structural motif]

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    233251571..233295674
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006712608.3XP_006712671.1  autophagy-related protein 16-1 isoform X2

    See identical proteins and their annotated locations for XP_006712671.1

    Conserved Domains (4) summary
    COG2319
    Location:248506
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:248538
    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 ...
    pfam13874
    Location:83140
    Nup54; Nucleoporin complex subunit 54
    sd00039
    Location:260297
    7WD40; WD40 repeat [structural motif]
  2. XM_005246084.2XP_005246141.1  autophagy-related protein 16-1 isoform X3

    See identical proteins and their annotated locations for XP_005246141.1

    Conserved Domains (3) summary
    COG2319
    Location:188446
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:188478
    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 ...
    sd00039
    Location:200237
    7WD40; WD40 repeat [structural motif]
  3. XM_005246086.2XP_005246143.1  autophagy-related protein 16-1 isoform X4

    See identical proteins and their annotated locations for XP_005246143.1

    UniProtKB/TrEMBL
    A0A024R4B6
    Related
    ENSP00000362625.5, ENST00000373525.9
    Conserved Domains (3) summary
    COG2319
    Location:171429
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:171461
    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 ...
    sd00039
    Location:183220
    7WD40; WD40 repeat [structural motif]

RNA

  1. XR_241242.3 RNA Sequence

  2. XR_001738801.2 RNA Sequence

    Related
    ENST00000392021.7

Reference GRCh38.p13 PATCHES

Genomic

  1. NW_011332690.1 Reference GRCh38.p13 PATCHES

    Range
    196909..241012
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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