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 asso... See more...

Aliases for ATAD3A Gene

Aliases for ATAD3A Gene

  • ATPase Family AAA Domain Containing 3A 2 3 5
  • ATPase Family AAA Domain-Containing Protein 3A 3 4
  • FLJ10709 2
  • PHRINL 3
  • ATAD3A 5
  • HAYOS 3

External Ids for ATAD3A Gene

Previous GeneCards Identifiers for ATAD3A Gene

  • GC01P001387
  • GC01P001532
  • GC01P001374
  • GC01P001439
  • GC01P000720
  • GC01P001447
  • GC01P001514

Summaries for ATAD3A Gene

Entrez Gene Summary for ATAD3A Gene

  • 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]

GeneCards Summary for ATAD3A Gene

ATAD3A (ATPase Family AAA Domain Containing 3A) is a Protein Coding gene. Diseases associated with ATAD3A include Harel-Yoon Syndrome and Pontocerebellar Hypoplasia, Hypotonia, And Respiratory Insufficiency Syndrome, Neonatal Lethal. An important paralog of this gene is ATAD3B.

UniProtKB/Swiss-Prot Summary for ATAD3A Gene

  • Essential for mitochondrial network organization, mitochondrial metabolism and cell growth at organism and cellular level. May play an important role in mitochondrial protein synthesis. May also participate in mitochondrial DNA replication. May bind to mitochondrial DNA D-loops and contribute to nucleoid stability. Required for enhanced channeling of cholesterol for hormone-dependent steroidogenesis.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATAD3A Gene

Genomics for ATAD3A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ATAD3A Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATAD3A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATAD3A

Top Transcription factor binding sites by QIAGEN in the ATAD3A gene promoter:
  • Arnt
  • Oct-B1
  • oct-B2
  • oct-B3
  • POU2F1
  • POU2F1a
  • POU2F2
  • POU2F2 (Oct-2.1)
  • POU2F2B
  • POU2F2C

Genomic Locations for ATAD3A Gene

Genomic Locations for ATAD3A Gene
chr1:1,512,143-1,534,687
(GRCh38/hg38)
Size:
22,545 bases
Orientation:
Plus strand
chr1:1,447,523-1,470,067
(GRCh37/hg19)
Size:
22,545 bases
Orientation:
Plus strand

Genomic View for ATAD3A Gene

Genes around ATAD3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATAD3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATAD3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATAD3A Gene

Proteins for ATAD3A Gene

  • Protein details for ATAD3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NVI7-ATD3A_HUMAN
    Recommended name:
    ATPase family AAA domain-containing protein 3A
    Protein Accession:
    Q9NVI7
    Secondary Accessions:
    • B3KPB3
    • D2K8Q1
    • G3V1I6
    • Q5SV23
    • Q8N275
    • Q96A50

    Protein attributes for ATAD3A Gene

    Size:
    634 amino acids
    Molecular mass:
    71369 Da
    Quaternary structure:
    • Can form homooligomers. Homodimer formation at the N-terminus may be regulated by ATP and is required for the interaction with the inner surface of the mitochondrial outer membrane and correct mitochondrial homeostasis. Interacts with components of the mitochondrial ribosome and with other proteins involved in mitochondrial RNA metabolism. May also interact with protein involved in lipid metabolism, including STARD9. May interact with FAM210A. Interacts with GADD45GIP1. Interacts with S100B in a Ca(+2)- and Zn(+2)-dependent manner; this interaction probably occurs in the cytosol prior to mitochondrial targeting. S100B could assist ATAD3A cytoplasmic processing, preventing aggregation and favoring mitochondrial localization. Interacts with HSP60/HSPD1. Forms heterooligomers with ATAD3B; this interaction may affect ATAD3A activity.
    Miscellaneous:
    • [Isoform 2]: May be the predominant ATAD3A form.

    Alternative splice isoforms for ATAD3A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ATAD3A Gene

Post-translational modifications for ATAD3A Gene

  • Ubiquitination at Lys406 and Lys621
  • Modification sites at PhosphoSitePlus

Other Protein References for ATAD3A Gene

Antibody Products

  • Abcam antibodies for ATAD3A

No data available for DME Specific Peptides for ATAD3A Gene

Domains & Families for ATAD3A Gene

Gene Families for ATAD3A Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for ATAD3A Gene

Suggested Antigen Peptide Sequences for ATAD3A Gene

GenScript: Design optimal peptide antigens:
  • ATPase family AAA domain-containing protein 3A (ATD3A_HUMAN)
  • ATPase family, AAA domain containing 3A, isoform CRA_b (D2K8Q1_HUMAN)
  • ATPase family, AAA domain containing 3A (Q5SV16_HUMAN)
  • ATPase family, AAA domain containing 3A (Q5SV24_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NVI7

UniProtKB/Swiss-Prot:

ATD3A_HUMAN :
  • The transmembrane domain and a C-terminal adjacent region contain all information necessary for mitochondrial targeting.
  • Belongs to the AAA ATPase family.
Domain:
  • The transmembrane domain and a C-terminal adjacent region contain all information necessary for mitochondrial targeting.
Family:
  • Belongs to the AAA ATPase family.
genes like me logo Genes that share domains with ATAD3A: view

Function for ATAD3A Gene

Molecular function for ATAD3A Gene

UniProtKB/Swiss-Prot Function:
Essential for mitochondrial network organization, mitochondrial metabolism and cell growth at organism and cellular level. May play an important role in mitochondrial protein synthesis. May also participate in mitochondrial DNA replication. May bind to mitochondrial DNA D-loops and contribute to nucleoid stability. Required for enhanced channeling of cholesterol for hormone-dependent steroidogenesis.
UniProtKB/Swiss-Prot Induction:
Up-regulated by Angiotensin/AGT.

Phenotypes From GWAS Catalog for ATAD3A Gene

Gene Ontology (GO) - Molecular Function for ATAD3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0005515 protein binding IPI 22664726
GO:0005524 ATP binding IEA --
GO:0008270 zinc ion binding IBA 21873635
genes like me logo Genes that share ontologies with ATAD3A: view
genes like me logo Genes that share phenotypes with ATAD3A: view

Human Phenotype Ontology for ATAD3A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ATAD3A Gene

MGI Knock Outs for ATAD3A:
  • Atad3a Atad3a<tm1a(KOMP)Wtsi>

Animal Model Products

CRISPR Products

miRNA for ATAD3A Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATAD3A

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for ATAD3A Gene

Localization for ATAD3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATAD3A Gene

Mitochondrion inner membrane. Single-pass membrane protein. Mitochondrion matrix, mitochondrion nucleoid. Note=In the mitochondrial inner membrane, enriched in sites with the potential to form contacts with the outer membrane (PubMed:20349121, PubMed:20154147). The N-terminal domain interacts with the inner surface of the mitochondrial outer membrane and the C-terminal domain localizes in a specific matrix compartment, where it is associated with nucleoids (PubMed:18063578). {ECO:0000269 PubMed:18063578, ECO:0000269 PubMed:20154147, ECO:0000269 PubMed:20349121}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATAD3A gene
Compartment Confidence
mitochondrion 5
cytosol 3
nucleus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ATAD3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA 20332122
GO:0005743 mitochondrial inner membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0042645 mitochondrial nucleoid IEA --
genes like me logo Genes that share ontologies with ATAD3A: view

Pathways & Interactions for ATAD3A Gene

PathCards logo

SuperPathways for ATAD3A Gene

No Data Available

Gene Ontology (GO) - Biological Process for ATAD3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001558 regulation of cell growth IMP 20332122
GO:0007005 mitochondrion organization IEA,IBA 21873635
GO:0043066 negative regulation of apoptotic process IMP 20332122
genes like me logo Genes that share ontologies with ATAD3A: view

No data available for Pathways by source and SIGNOR curated interactions for ATAD3A Gene

Drugs & Compounds for ATAD3A Gene

No Compound Related Data Available

Transcripts for ATAD3A Gene

mRNA/cDNA for ATAD3A Gene

3 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATAD3A

Alternative Splicing Database (ASD) splice patterns (SP) for ATAD3A Gene

No ASD Table

Relevant External Links for ATAD3A Gene

GeneLoc Exon Structure for
ATAD3A

Expression for ATAD3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ATAD3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Lymph (Hematopoietic System)

Protein differential expression in normal tissues from HIPED for ATAD3A Gene

This gene is overexpressed in Nasal epithelium (21.6) and Bone (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ATAD3A Gene



Protein tissue co-expression partners for ATAD3A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATAD3A

SOURCE GeneReport for Unigene cluster for ATAD3A Gene:

Hs.23413

mRNA Expression by UniProt/SwissProt for ATAD3A Gene:

Q9NVI7-ATD3A_HUMAN
Tissue specificity: Overexpressed in lung adenocarcinomas (at protein level).

Evidence on tissue expression from TISSUES for ATAD3A Gene

  • Nervous system(4.7)
  • Skin(4.5)
genes like me logo Genes that share expression patterns with ATAD3A: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATAD3A Gene

Orthologs for ATAD3A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ATAD3A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ATAD3B 30
  • 97.38 (n)
-- 31
  • 80 (a)
ManyToMany
Dog
(Canis familiaris)
Mammalia ATAD3A 31
  • 91 (a)
OneToMany
ATAD3B 30
  • 86.61 (n)
Cow
(Bos Taurus)
Mammalia ATAD3 31
  • 90 (a)
OneToMany
ATAD3A 30
  • 87.65 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 88 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Atad3a 30
  • 84.39 (n)
Mouse
(Mus musculus)
Mammalia Atad3a 30 17 31
  • 83.36 (n)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 81 (a)
OneToMany
Chicken
(Gallus gallus)
Aves -- 31
  • 80 (a)
OneToMany
ATAD3A 30
  • 77.03 (n)
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 80 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia atad3a 30
  • 71.79 (n)
Str.16479 30
African clawed frog
(Xenopus laevis)
Amphibia MGC68616 30
Zebrafish
(Danio rerio)
Actinopterygii atad3b 30 31
  • 76.14 (n)
OneToMany
Dr.25732 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001792 30
  • 67.05 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta bor 30 31
  • 65.84 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea atad-3 30 31
  • 55.6 (n)
OneToMany
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT3G03060 30
  • 48.78 (n)
Rice
(Oryza sativa)
Liliopsida Os02g0697600 30
  • 49.68 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.6689 31
  • 65 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.5657 30
Species where no ortholog for ATAD3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for ATAD3A Gene

ENSEMBL:
Gene Tree for ATAD3A (if available)
TreeFam:
Gene Tree for ATAD3A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATAD3A: view image

Paralogs for ATAD3A Gene

Paralogs for ATAD3A Gene

(3) SIMAP similar genes for ATAD3A Gene using alignment to 3 proteins:

  • ATD3A_HUMAN
  • H0Y2W2_HUMAN
  • Q5SV16_HUMAN

Pseudogenes.org Pseudogenes for ATAD3A Gene

genes like me logo Genes that share paralogs with ATAD3A: view

Variants for ATAD3A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATAD3A Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
637018 Pathogenic: Congenital cerebellar hypoplasia; PONTOCEREBELLAR HYPOPLASIA, HYPOTONIA, AND RESPIRATORY INSUFFICIENCY SYNDROME, NEONATAL LETHAL 1,525,242(+) T/G MISSENSE_VARIANT
709201 Benign: not provided 1,512,313(+) C/T SYNONYMOUS_VARIANT
713029 Likely Benign: not provided 1,525,291(+) C/T SYNONYMOUS_VARIANT
719313 Benign: not provided 1,534,060(+) C/T SYNONYMOUS_VARIANT
721370 Likely Benign: not provided 1,534,043(+) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for ATAD3A Gene

Structural Variations from Database of Genomic Variants (DGV) for ATAD3A Gene

Variant ID Type Subtype PubMed ID
dgv2e212 CNV loss 25503493
esv2658581 CNV deletion 23128226
esv2758913 CNV gain+loss 17122850
esv3549676 CNV deletion 23714750
esv3585000 CNV loss 21293372
esv3585001 CNV loss 21293372
nsv1009541 CNV gain 25217958
nsv1011818 CNV gain 25217958
nsv10161 CNV gain+loss 18304495
nsv1074453 CNV deletion 25765185
nsv1136055 CNV deletion 24896259
nsv482157 CNV gain 20164927
nsv482937 CNV loss 15286789
nsv545000 CNV loss 21841781
nsv545010 CNV loss 21841781
nsv821920 CNV gain 20364138
nsv945744 CNV duplication 23825009
nsv950452 CNV deletion 24416366

Variation tolerance for ATAD3A Gene

Residual Variation Intolerance Score: 91.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.22; 81.04% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATAD3A Gene

Human Gene Mutation Database (HGMD)
ATAD3A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATAD3A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATAD3A Gene

Disorders for ATAD3A Gene

MalaCards: The human disease database

(14) MalaCards diseases for ATAD3A Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

UniProtKB/Swiss-Prot

ATD3A_HUMAN
  • Harel-Yoon syndrome (HAYOS) [MIM:617183]: A syndrome characterized by global developmental delay, hypotonia, intellectual disability, and axonal neuropathy. Some patients have optic atrophy and hypertrophic cardiomyopathy. HAYOS inheritance can be autosomal dominant or autosomal recessive. {ECO:0000269 PubMed:27640307}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for ATAD3A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with ATAD3A: view

No data available for Genatlas for ATAD3A Gene

Publications for ATAD3A Gene

  1. ATPase-deficient mitochondrial inner membrane protein ATAD3A disturbs mitochondrial dynamics in dominant hereditary spastic paraplegia. (PMID: 28158749) Cooper HM … Tyynismaa H (Human molecular genetics 2017) 2 3
  2. Recurrent De Novo and Biallelic Variation of ATAD3A, Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes. (PMID: 27640307) Harel T … Lupski JR (American journal of human genetics 2016) 3 4
  3. ATAD3B is a human embryonic stem cell specific mitochondrial protein, re-expressed in cancer cells, that functions as dominant negative for the ubiquitous ATAD3A. (PMID: 22664726) Merle N … Baudier J (Mitochondrion 2012) 3 4
  4. Topological analysis of ATAD3A insertion in purified human mitochondria. (PMID: 20349121) Hubstenberger A … Rousseau D (Journal of bioenergetics and biomembranes 2010) 3 4
  5. The AAA+ ATPase ATAD3A controls mitochondrial dynamics at the interface of the inner and outer membranes. (PMID: 20154147) Gilquin B … Baudier J (Molecular and cellular biology 2010) 3 4

Products for ATAD3A Gene

  • Signalway Proteins for ATAD3A

Sources for ATAD3A Gene