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

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; AllianceGenome:HGNC:21498
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: mouse all
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Genomic context

Location:: 2q37.1

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (233251673..233295669)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (233739756..233783753)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (234160319..234204315)

Chromosome 2 - NC_000002.12 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Reticulophagy mediated by the V-ATPase-ATG16L1-LC3C axis.
Title: Reticulophagy mediated by the V-ATPase-ATG16L1-LC3C axis.
WIPI2b recruitment to phagophores and ATG16L1 binding are regulated by ULK1 phosphorylation.
Title: WIPI2b recruitment to phagophores and ATG16L1 binding are regulated by ULK1 phosphorylation.
Estrogen receptor is involved in the osteoarthritis mediated by Atg16L1-NLRP3 activation.
Title: Estrogen receptor is involved in the osteoarthritis mediated by Atg16L1-NLRP3 activation.
Macrophage ATG16L1 expression suppresses metabolic dysfunction-associated steatohepatitis progression by promoting lipophagy.
Title: Macrophage ATG16L1 expression suppresses metabolic dysfunction-associated steatohepatitis progression by promoting lipophagy.
Lens autophagy protein ATG16L1: a potential target for cataract treatment.
Title: Lens autophagy protein ATG16L1: a potential target for cataract treatment.
Autophagy-enhancing ATG16L1 polymorphism is associated with improved clinical outcome and T-cell immunity in chronic HIV-1 infection.
Title: Autophagy-enhancing ATG16L1 polymorphism is associated with improved clinical outcome and T-cell immunity in chronic HIV-1 infection.
Association of ATG10 rs1864183, ATG16L1 rs2241880 and miR-126 with esophageal cancer.
Title: Association of ATG10 rs1864183, ATG16L1 rs2241880 and miR-126 with esophageal cancer.
ATG16L1 rs2241880/T300A increases susceptibility to perianal Crohn's disease: An updated meta-analysis on inflammatory bowel disease risk and clinical outcomes.
Title: ATG16L1 rs2241880/T300A increases susceptibility to perianal Crohn's disease: An updated meta-analysis on inflammatory bowel disease risk and clinical outcomes.
Association of ATG16L1 and ATG5 gene polymorphisms with susceptibility to hepatitis B virus infection and progression to HCC in central China.
Title: Association of ATG16L1 and ATG5 gene polymorphisms with susceptibility to hepatitis B virus infection and progression to HCC in central China.
The V-ATPase-ATG16L1 axis recruits LRRK2 to facilitate the lysosomal stress response.
Title: The V-ATPase-ATG16L1 axis recruits LRRK2 to facilitate the lysosomal stress response.

Submit: New GeneRIF Correction See all GeneRIFs (197)

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

Associated conditions

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

EBI GWAS Catalog

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

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

D2S1507E (e-PCR)
- UniSTS:66655

WI-12735 (e-PCR)
- UniSTS:56956

WI-11277 (e-PCR)
- UniSTS:23445

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-membrane adaptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein-membrane adaptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables ubiquitin-like protein transferase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in C-terminal protein lipidation	IDA Inferred from Direct Assay more info	PubMed
involved_in autophagosome assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in autophagosome assembly	ISO Inferred from Sequence Orthology more info
involved_in autophagosome assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in axonal transport	IEA Inferred from Electronic Annotation more info
involved_in corpus callosum development	IEA Inferred from Electronic Annotation more info
involved_in defense response to virus	IEA Inferred from Electronic Annotation more info
involved_in hippocampus development	IEA Inferred from Electronic Annotation more info
involved_in macroautophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in macroautophagy	ISO Inferred from Sequence Orthology more info
involved_in macroautophagy	TAS Traceable Author Statement more info
involved_in microautophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in negative stranded viral RNA replication	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of autophagy	IEA Inferred from Electronic Annotation more info
involved_in protein localization to phagophore assembly site	IEA Inferred from Electronic Annotation more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in xenophagy	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of Atg12-Atg5-Atg16 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Atg12-Atg5-Atg16 complex	IDA Inferred from Direct Assay more info	PubMed
part_of Atg12-Atg5-Atg16 complex	IPI Inferred from Physical Interaction more info	PubMed
located_in autophagosome	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in autophagosome membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in autophagosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in axon	IEA Inferred from Electronic Annotation more info
located_in axoneme	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	TAS Traceable Author Statement more info
is_active_in endolysosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in phagophore assembly site membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in phagophore assembly site membrane	ISO Inferred from Sequence Orthology more info
located_in sperm midpiece	ISS Inferred from Sequence or Structural Similarity more info
located_in vacuole-isolation membrane contact site	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: autophagy-related protein 16-1

Names: APG16L beta; ATG16 autophagy related 16-like 1; WD repeat domain 30

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.

Genomic

NG_023038.1 RefSeqGene

Range

5103..49099

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001190266.2 → NP_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/TrEMBL

Q17RG0, Q53SV2

Conserved Domains (3) summary

cd00200
Location:231 → 521

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:243 → 280

7WD40; WD40 repeat [structural motif]

pfam08614
Location:2 → 122

ATG16; Autophagy protein 16 (ATG16)
NM_001190267.2 → NP_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/TrEMBL

Q17RG0

Conserved Domains (4) summary

COG2319
Location:199 → 457

WD40; WD40 repeat [General function prediction only]

cd00200
Location:199 → 489

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:211 → 248

7WD40; WD40 repeat [structural motif]

cl23720
Location:1 → 110

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
NM_001363742.2 → NP_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

UniProtKB/TrEMBL

A5YM60, E7EVC7, L7UQD0

Related

ENSP00000375873.1, ENST00000392018.1

Conserved Domains (4) summary

COG2319
Location:272 → 390

WD40; WD40 repeat [General function prediction only]

cd00200
Location:332 → 622

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:344 → 381

7WD40; WD40 repeat [structural motif]

pfam08614
Location:31 → 206

ATG16; Autophagy protein 16 (ATG16)
NM_017974.4 → NP_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/TrEMBL

A5YM60, L7UQD0

Related

ENSP00000375875.4, ENST00000392020.8

Conserved Domains (3) summary

cd00200
Location:296 → 586

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:308 → 345

7WD40; WD40 repeat [structural motif]

pfam08614
Location:31 → 206

ATG16; Autophagy protein 16 (ATG16)
NM_030803.7 → NP_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

A3EXK9, A3EXL0, B6ZDH0, Q676U5, Q6IPN1, Q6UXW4, Q6ZVZ5, Q8NCY2, Q96JV5, Q9H619

UniProtKB/TrEMBL

A5YM60, L7UQD0

Related

ENSP00000375872.4, ENST00000392017.9

Conserved Domains (5) summary

COG2319
Location:315 → 573

WD40; WD40 repeat [General function prediction only]

cd00200
Location:315 → 605

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:31 → 206

ATG16; Autophagy protein 16 (ATG16)

sd00039
Location:327 → 364

7WD40; WD40 repeat [structural motif]

cl23720
Location:117 → 222

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
NM_198890.3 → NP_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)

AC013726, BC071846, DB084962, EF079890

Consensus CDS

CCDS54438.1

UniProtKB/Swiss-Prot

Q676U5

Related

ENSP00000318259.6, ENST00000347464.9

Conserved Domains (3) summary

COG2319
Location:152 → 410

WD40; WD40 repeat [General function prediction only]

cd00200
Location:152 → 442

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:164 → 201

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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

233251673..233295669

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006712608.4 → XP_006712671.1 autophagy-related protein 16-1 isoform X1

See identical proteins and their annotated locations for XP_006712671.1

UniProtKB/TrEMBL

A5YM60, L7UQD0

Conserved Domains (4) summary

COG2319
Location:248 → 506

WD40; WD40 repeat [General function prediction only]

cd00200
Location:248 → 538

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:83 → 140

Nup54; Nucleoporin complex subunit 54

sd00039
Location:260 → 297

7WD40; WD40 repeat [structural motif]
XM_047444848.1 → XP_047300804.1 autophagy-related protein 16-1 isoform X2

UniProtKB/TrEMBL

A5YM60, L7UQD0
XM_047444849.1 → XP_047300805.1 autophagy-related protein 16-1 isoform X3

UniProtKB/TrEMBL

A5YM60, L7UQD0
XM_005246084.3 → XP_005246141.1 autophagy-related protein 16-1 isoform X4

See identical proteins and their annotated locations for XP_005246141.1

Conserved Domains (3) summary

COG2319
Location:188 → 446

WD40; WD40 repeat [General function prediction only]

cd00200
Location:188 → 478

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:200 → 237

7WD40; WD40 repeat [structural motif]
XM_005246086.3 → XP_005246143.1 autophagy-related protein 16-1 isoform X5

See identical proteins and their annotated locations for XP_005246143.1

Related

ENSP00000362625.5, ENST00000373525.9

Conserved Domains (3) summary

COG2319
Location:171 → 429

WD40; WD40 repeat [General function prediction only]

cd00200
Location:171 → 461

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:183 → 220

7WD40; WD40 repeat [structural motif]
XM_047444850.1 → XP_047300806.1 autophagy-related protein 16-1 isoform X6

Reference GRCh38.p14 PATCHES

Genomic

NW_011332690.1 Reference GRCh38.p14 PATCHES

Range

197011..241007

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331682.1 → XP_054187657.1 autophagy-related protein 16-1 isoform X1

UniProtKB/TrEMBL

A5YM60, L7UQD0
XM_054331683.1 → XP_054187658.1 autophagy-related protein 16-1 isoform X2

UniProtKB/TrEMBL

A5YM60, L7UQD0
XM_054331684.1 → XP_054187659.1 autophagy-related protein 16-1 isoform X3

UniProtKB/TrEMBL

A5YM60, L7UQD0
XM_054331685.1 → XP_054187660.1 autophagy-related protein 16-1 isoform X4
XM_054331686.1 → XP_054187661.1 autophagy-related protein 16-1 isoform X5
XM_054331687.1 → XP_054187662.1 autophagy-related protein 16-1 isoform X6

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

233739756..233783753

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054342708.1 → XP_054198683.1 autophagy-related protein 16-1 isoform X1

UniProtKB/TrEMBL

A5YM60, L7UQD0
XM_054342709.1 → XP_054198684.1 autophagy-related protein 16-1 isoform X2

UniProtKB/TrEMBL

A5YM60, L7UQD0
XM_054342710.1 → XP_054198685.1 autophagy-related protein 16-1 isoform X3

UniProtKB/TrEMBL

A5YM60, L7UQD0
XM_054342711.1 → XP_054198686.1 autophagy-related protein 16-1 isoform X4
XM_054342712.1 → XP_054198687.1 autophagy-related protein 16-1 isoform X5
XM_054342713.1 → XP_054198688.1 autophagy-related protein 16-1 isoform X6