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

Summary

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 and negative stranded viral RNA replication. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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

Location:: 11q13.4

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (72814411..72843740)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (72742639..72773369)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (72525456..72540680)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The role of ATG16L2 in autophagy and disease.
Title: The role of ATG16L2 in autophagy and disease.
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.
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.
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.
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.
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.
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.
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.

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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 EBI GWAS CatalogPubMed
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SGC32787 (e-PCR)
- UniSTS:45622

G30987 (e-PCR)
- UniSTS:67665

RH45037 (e-PCR)
- UniSTS:37767

Homology

Orthologs from Annotation Pipeline: 234 organisms have orthologs with human gene ATG16L2
Orthologs

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in autophagosome assembly	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in protein lipidation	IDA Inferred from Direct Assay more info	PubMed
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
is_active_in autophagosome membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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)

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]
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

Q8NAA4, Q8NBG0

UniProtKB/TrEMBL

Q9H7Q5

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_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

72814411..72843740

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]
XM_047427840.1 → XP_047283796.1 protein Atg16l2 isoform X4
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]
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]
XM_047427841.1 → XP_047283797.1 protein Atg16l2 isoform X6
XM_006718733.4 → XP_006718796.1 protein Atg16l2 isoform X7

Conserved Domains (1) summary

pfam08614
Location:17 → 203

ATG16; Autophagy protein 16 (ATG16)
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]
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]
XM_047427842.1 → XP_047283798.1 protein Atg16l2 isoform X8