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    ATAD3A ATPase family AAA domain containing 3A [ Homo sapiens (human) ]

    Gene ID: 55210, updated on 3-Nov-2024

    Summary

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    Official Symbol
    ATAD3Aprovided by HGNC
    Official Full Name
    ATPase family AAA domain containing 3Aprovided by HGNC
    Primary source
    HGNC:HGNC:25567
    See related
    Ensembl:ENSG00000197785 MIM:612316; AllianceGenome:HGNC:25567
    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
    HAYOS; PHRINL
    Summary
    This gene encodes a ubiquitously expressed mitochondrial membrane protein that contributes to mitochondrial dynamics, nucleoid organization, protein translation, cell growth, and cholesterol metabolism. This gene is a member of the ATPase family AAA-domain containing 3 gene family which, in humans, includes two other paralogs. Naturally occurring mutations in this gene are associated with distinct neurological syndromes including Harel-Yoon syndrome. High-level expression of this gene is associated with poor survival in breast cancer patients. A homozygous knockout of the orthologous gene in mice results in embryonic lethality at day 7.5 due to growth retardation and defective development of the trophoblast lineage. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
    Expression
    Ubiquitous expression in bone marrow (RPKM 6.3), testis (RPKM 6.2) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ATAD3A in Genome Data Viewer
    Location:
    1p36.33
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1512162..1534685)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (946666..969189)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1447542..1470065)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1389959-1390458 Neighboring gene ATPase family AAA domain containing 3C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1397006-1397780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 75 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1409130-1409976 Neighboring gene ATPase family AAA domain containing 3B Neighboring gene MPRA-validated peak11 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1443749-1444392 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1444393-1445034 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 76 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 77 Neighboring gene Sharpr-MPRA regulatory region 185 Neighboring gene transmembrane protein 240 Neighboring gene SSU72 homolog, RNA polymerase II CTD phosphatase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1505865-1506366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 78 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 79

    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. Yeast-based production and purification of HIS-tagged human ATAD3A, A specific target of S100B. Li S, et al. Protein Expr Purif, 2012 Jun. PMID 22542587
    2. Recurrent De Novo NAHR Reciprocal Duplications in the ATAD3 Gene Cluster Cause a Neurogenetic Trait with Perturbed Cholesterol and Mitochondrial Metabolism. Gunning AC, et al. Am J Hum Genet, 2020 Feb 6. PMID 32004445, Free PMC Article
    3. Using Genome-Editing Tools to Develop a Novel In Situ Coincidence Reporter Assay for Screening ATAD3A Transcriptional Inhibitors. Lang L, et al. Methods Mol Biol, 2020. PMID 32219745, Free PMC Article
    4. Novel ATAD3A recessive mutation associated to fatal cerebellar hypoplasia with multiorgan involvement and mitochondrial structural abnormalities. Peralta S, et al. Mol Genet Metab, 2019 Dec. PMID 31727539
    5. Mitochondrial dysfunction caused by novel ATAD3A mutations. Dorison N, et al. Mol Genet Metab, 2020 Sep-Oct. PMID 32933822

    See all (259) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PERK-ATAD3A interaction provides a subcellular safe haven for protein synthesis during ER stress.
      Title: PERK-ATAD3A interaction provides a subcellular safe haven for protein synthesis during ER stress.
    2. Identification of ATAD3A as a key regulator in non-small cell lung cancer by promoting STAT3-induced cell proliferation and tumor angiogenesis.
      Title: Identification of ATAD3A as a key regulator in non-small cell lung cancer by promoting STAT3-induced cell proliferation and tumor angiogenesis.
    3. The value of ATAD3A as a potential biomarker for bladder cancer.
      Title: The value of ATAD3A as a potential biomarker for bladder cancer.
    4. "ATAD3C regulates ATAD3A assembly and function in the mitochondrial membrane".
      Title: "ATAD3C regulates ATAD3A assembly and function in the mitochondrial membrane".
    5. ATAD3A-related pontocerebellar hypoplasia: new patients and insights into phenotypic variability.
      Title: ATAD3A-related pontocerebellar hypoplasia: new patients and insights into phenotypic variability.
    6. Targeting ATAD3A-PINK1-mitophagy axis overcomes chemoimmunotherapy resistance by redirecting PD-L1 to mitochondria.
      Title: Targeting ATAD3A-PINK1-mitophagy axis overcomes chemoimmunotherapy resistance by redirecting PD-L1 to mitochondria.
    7. The oncoprotein MUC1 facilitates breast cancer progression by promoting Pink1-dependent mitophagy via ATAD3A destabilization.
      Title: The oncoprotein MUC1 facilitates breast cancer progression by promoting Pink1-dependent mitophagy via ATAD3A destabilization.
    8. ATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly.
      Title: ATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly.
    9. Functional interpretation of ATAD3A variants in neuro-mitochondrial phenotypes.
      Title: Functional interpretation of ATAD3A variants in neuro-mitochondrial phenotypes.
    10. Enhanced cGAS-STING-dependent interferon signaling associated with mutations in ATAD3A.
      Title: Enhanced cGAS-STING-dependent interferon signaling associated with mutations in ATAD3A.
    Submit: New GeneRIF Correction See all GeneRIFs (38)

    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
    Harel-Yoon syndrome
    MedGen: C4310677 OMIM: 617183 GeneReviews: Not available
    		not available
    Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal
    MedGen: C5394137 OMIM: 618810 GeneReviews: Not available
    		not available

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpu vpu HIV-1 Vpu is identified to have a physical interaction with ATPase family, AAA domain containing 3A (ATAD3A) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses 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

    Homology

    Clone Names

    • FLJ10709, FLJ35514

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of HRI-mediated signaling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in antiviral innate immune response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrion organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial nucleoid IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ATPase family AAA domain-containing protein 3A

    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

    1. NG_053035.1 RefSeqGene

      Range
      5020..27543
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001170535.3 → NP_001164006.1  ATPase family AAA domain-containing protein 3A isoform 2

      See identical proteins and their annotated locations for NP_001164006.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.
      Source sequence(s)
      AK001571, BC011814, BC014101, DA206969
      Consensus CDS
      CCDS53259.1
      UniProtKB/TrEMBL
      Q96T67
      Related
      ENSP00000368031.3, ENST00000378756.8
      Conserved Domains (3) summary
      smart00382
      Location:346 → 476
      AAA; ATPases associated with a variety of cellular activities
      pfam00004
      Location:348 → 475
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam12037
      Location:42 → 286
      DUF3523; Domain of unknown function (DUF3523)

    2. NM_001170536.3 → NP_001164007.1  ATPase family AAA domain-containing protein 3A isoform 3

      See identical proteins and their annotated locations for NP_001164007.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences in the 5' UTR and 5' coding region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AK001571, AK056099, BC011814, BC014101
      Consensus CDS
      CCDS53260.1
      UniProtKB/TrEMBL
      Q96T67
      Related
      ENSP00000439290.1, ENST00000536055.6
      Conserved Domains (3) summary
      smart00382
      Location:267 → 397
      AAA; ATPases associated with a variety of cellular activities
      pfam00004
      Location:269 → 396
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam12037
      Location:12 → 207
      DUF3523; Domain of unknown function (DUF3523)

    3. NM_018188.5 → NP_060658.3  ATPase family AAA domain-containing protein 3A isoform 1

      See identical proteins and their annotated locations for NP_060658.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK001571, AK091144, BC011814, BC014101, DA206969
      Consensus CDS
      CCDS31.1
      UniProtKB/Swiss-Prot
      B3KPB3, D2K8Q1, G3V1I6, Q5SV23, Q8N275, Q96A50, Q9NVI7
      UniProtKB/TrEMBL
      Q96T67
      Related
      ENSP00000368030.5, ENST00000378755.9
      Conserved Domains (3) summary
      smart00382
      Location:394 → 524
      AAA; ATPases associated with a variety of cellular activities
      pfam00004
      Location:396 → 523
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam12037
      Location:42 → 334
      DUF3523; Domain of unknown function (DUF3523)

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      1512162..1534685
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047424288.1 → XP_047280244.1  ATPase family AAA domain-containing protein 3A isoform X1

    2. XM_047424289.1 → XP_047280245.1  ATPase family AAA domain-containing protein 3A isoform X2

    3. XM_047424290.1 → XP_047280246.1  ATPase family AAA domain-containing protein 3A isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      946666..969189
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337419.1 → XP_054193394.1  ATPase family AAA domain-containing protein 3A isoform X1

    2. XM_054337420.1 → XP_054193395.1  ATPase family AAA domain-containing protein 3A isoform X2

    3. XM_054337421.1 → XP_054193396.1  ATPase family AAA domain-containing protein 3A isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NVI7.2 GenPept UniProtKB/Swiss-Prot:Q9NVI7

    Gene LinkOut

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

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