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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
    mouse all
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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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    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)

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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