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ATG9A autophagy related 9A [ Homo sapiens (human) ]

Gene ID: 79065, updated on 2-Nov-2024

Summary

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Official Symbol
ATG9Aprovided by HGNC
Official Full Name
autophagy related 9Aprovided by HGNC
Primary source
HGNC:HGNC:22408
See related
Ensembl:ENSG00000198925 MIM:612204; AllianceGenome:HGNC:22408
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
mATG9; APG9L1; MGD3208
Summary
Enables phospholipid scramblase activity. Involved in autophagosome assembly. Located in several cellular components, including Golgi apparatus; endosome; and phagophore assembly site. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in testis (RPKM 45.2), brain (RPKM 19.5) and 25 other tissues See more
Orthologs
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Genomic context

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See ATG9A in Genome Data Viewer
Location:
2q35
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (219219380..219229636, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (219704146..219714401, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (220084102..220094358, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12347 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220072463-220072962 Neighboring gene zinc finger AN1-type containing 2B Neighboring gene ATP binding cassette subfamily B member 6 (LAN blood group) Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:220082897-220083764 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220093298-220093846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220093847-220094394 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:220094395-220094942 Neighboring gene ankyrin repeat and zinc finger peptidyl tRNA hydrolase 1 Neighboring gene galactosidase beta 1 like Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:220109882-220110464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17145 Neighboring gene serine/threonine kinase 16 Neighboring gene tubulin alpha 4a

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. ATG9A overexpression is associated with disease recurrence and poor survival in patients with oral squamous cell carcinoma. Tang JY, et al. Virchows Arch, 2013 Dec. PMID 24085552
  2. Ultrasound cardiogram-based diagnosis of cardiac hypertrophy from hypertension and analysis of its relationship with expression of autophagy-related protein. Li S, et al. Ann Palliat Med, 2022 Feb. PMID 35249346
  3. The core autophagy protein ATG9A controls dynamics of cell protrusions and directed migration. Campisi D, et al. J Cell Biol, 2022 Mar 7. PMID 35180289, Free PMC Article
  4. Structure, lipid scrambling activity and role in autophagosome formation of ATG9A. Maeda S, et al. Nat Struct Mol Biol, 2020 Dec. PMID 33106659, Free PMC Article
  5. The HIF target ATG9A is essential for epithelial barrier function and tight junction biogenesis. Dowdell AS, et al. Mol Biol Cell, 2020 Sep 15. PMID 32726170, Free PMC Article

See all (118) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Tracking the transition from an ATG9A vesicle to an autophagosome.
    Title: Tracking the transition from an ATG9A vesicle to an autophagosome.
  2. NDRG1 overcomes resistance to immunotherapy of pancreatic ductal adenocarcinoma through inhibiting ATG9A-dependent degradation of MHC-1.
    Title: NDRG1 overcomes resistance to immunotherapy of pancreatic ductal adenocarcinoma through inhibiting ATG9A-dependent degradation of MHC-1.
  3. ATG9B is a tissue-specific homotrimeric lipid scramblase that can compensate for ATG9A.
    Title: ATG9B is a tissue-specific homotrimeric lipid scramblase that can compensate for ATG9A.
  4. ATG9A modulated by miR-195-5p can boost the malignant progression of cervical cancer cells.
    Title: ATG9A modulated by miR-195-5p can boost the malignant progression of cervical cancer cells.
  5. A novel role of ATG9A and RB1CC1/FIP200 in mediating cell-death checkpoints to repress TNF cytotoxicity.
    Title: A novel role of ATG9A and RB1CC1/FIP200 in mediating cell-death checkpoints to repress TNF cytotoxicity.
  6. Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation.
    Title: Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation.
  7. Atg9A-mediated mitophagy is required for decidual differentiation of endometrial stromal cells.
    Title: Atg9A-mediated mitophagy is required for decidual differentiation of endometrial stromal cells.
  8. RUSC2 and WDR47 oppositely regulate kinesin-1-dependent distribution of ATG9A to the cell periphery.
    Title: RUSC2 and WDR47 oppositely regulate kinesin-1-dependent distribution of ATG9A to the cell periphery.
  9. Ultrasound cardiogram-based diagnosis of cardiac hypertrophy from hypertension and analysis of its relationship with expression of autophagy-related protein.
    Title: Ultrasound cardiogram-based diagnosis of cardiac hypertrophy from hypertension and analysis of its relationship with expression of autophagy-related protein.
  10. The core autophagy protein ATG9A controls dynamics of cell protrusions and directed migration.
    Title: The core autophagy protein ATG9A controls dynamics of cell protrusions and directed migration.
Submit: New GeneRIF Correction See all GeneRIFs (51)

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

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

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

Potential readthrough

Included gene: ABCB6

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phospholipid scramblase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in autophagosome assembly IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in bone morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in mitophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in piecemeal microautophagy of the nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in plasma membrane phospholipid scrambling IEA
Inferred from Electronic Annotation
more info
  
involved_in programmed necrotic cell death ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein localization to phagophore assembly site IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in reticulophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in autophagosome IBA
Inferred from Biological aspect of Ancestor
more info
  
NOT located_in autophagosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in late endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in late endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in membrane HDA PubMed 
located_in mitochondrial membrane IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in phagophore assembly site IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in phagophore assembly site IDA
Inferred from Direct Assay
more info
 PubMed 
located_in phagophore assembly site membrane TAS
Traceable Author Statement
more info
  
located_in recycling endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in recycling endosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in trans-Golgi network IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
autophagy-related protein 9A
Names
APG9 autophagy 9-like 1
APG9-like 1
ATG9 autophagy related 9 homolog A
autophagy 9-like 1 protein

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_001077198.3 → NP_001070666.1  autophagy-related protein 9A

    See identical proteins and their annotated locations for NP_001070666.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) and variant 2 encode the same protein.
    Source sequence(s)
    BC065534, BK004018, DC347583
    Consensus CDS
    CCDS42820.1
    UniProtKB/Swiss-Prot
    Q3ZAQ6, Q6P0N7, Q7Z317, Q7Z320, Q7Z3C6, Q8NDK6, Q8WU65, Q9BVL5, Q9H6L1, Q9HAG7
    UniProtKB/TrEMBL
    B3KPP7
    Related
    ENSP00000355173.4, ENST00000361242.9
    Conserved Domains (1) summary
    pfam04109
    Location:37 → 525
    APG9; Autophagy protein Apg9

  2. NM_024085.5 → NP_076990.4  autophagy-related protein 9A

    See identical proteins and their annotated locations for NP_076990.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an internal exon in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC065534, BX538192, DC347583
    Consensus CDS
    CCDS42820.1
    UniProtKB/Swiss-Prot
    Q3ZAQ6, Q6P0N7, Q7Z317, Q7Z320, Q7Z3C6, Q8NDK6, Q8WU65, Q9BVL5, Q9H6L1, Q9HAG7
    UniProtKB/TrEMBL
    B3KPP7
    Related
    ENSP00000379983.2, ENST00000396761.6
    Conserved Domains (1) summary
    pfam04109
    Location:37 → 525
    APG9; Autophagy protein Apg9

RNA

  1. NR_104255.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate splice site in the central region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC001206, BC065534, DC347583
    Related
    ENST00000409033.7

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    219219380..219229636 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    219704146..219714401 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z3C6.3 GenPept UniProtKB/Swiss-Prot:Q7Z3C6

Gene LinkOut

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Chemical Information
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