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Aliases for NDUFA9 Gene

Aliases for NDUFA9 Gene

  • NADH:Ubiquinone Oxidoreductase Subunit A9 2 3 5
  • NADH Dehydrogenase (Ubiquinone) 1 Alpha Subcomplex, 9, 39kDa 2 3
  • Short Chain Dehydrogenase/Reductase Family 22E, Member 1 2 3
  • NADH-Ubiquinone Oxidoreductase 39 KDa Subunit 3 4
  • Complex I 39kDa Subunit 2 3
  • NDUFS2L 3 4
  • CI-39kD 3 4
  • NADH Dehydrogenase (Ubiquinone) Fe-S Protein 2-Like (NADH-Coenzyme Q Reductase) 3
  • NADH Dehydrogenase [Ubiquinone] 1 Alpha Subcomplex Subunit 9, Mitochondrial 3
  • NADH Dehydrogenase (Ubiquinone) 1 Alpha Subcomplex, 9 (39kD) 2
  • Complex I-39kD 4
  • SDR22E1 3
  • CI-39k 3
  • CI39k 3
  • CC6 3

External Ids for NDUFA9 Gene

Previous HGNC Symbols for NDUFA9 Gene


Previous GeneCards Identifiers for NDUFA9 Gene

  • GC12P004495
  • GC12P004650
  • GC12P004628
  • GC12P004759
  • GC12P004714
  • GC12P004760

Summaries for NDUFA9 Gene

Entrez Gene Summary for NDUFA9 Gene

  • The encoded protein is a subunit of the hydrophobic protein fraction of the NADH:ubiquinone oxidoreductase (complex I), the first enzyme complex in the electron transport chain located in the inner mitochondrial membrane. A pseudogene has been identified on chromosome 12. [provided by RefSeq, May 2010]

GeneCards Summary for NDUFA9 Gene

NDUFA9 (NADH:Ubiquinone Oxidoreductase Subunit A9) is a Protein Coding gene. Diseases associated with NDUFA9 include Leigh Syndrome and Leigh Syndrome With Leukodystrophy. Among its related pathways are Metabolism and Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor. An important paralog of this gene is ENSG00000255639.

UniProtKB/Swiss-Prot for NDUFA9 Gene

  • Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Gene Wiki entry for NDUFA9 Gene

Additional gene information for NDUFA9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NDUFA9 Gene

Genomics for NDUFA9 Gene

GeneHancer (GH) Regulatory Elements for NDUFA9 Gene

Promoters and enhancers for NDUFA9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J004647 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 0.0 -43 2.4 PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 POLR2B ZNF207 AKAP3 NDUFA9 GC12P005806 LOC103568124 GALNT8 GAU1 DYRK4 LOC100420673 ENSG00000256381 ENSG00000272921
GH12J004564 Enhancer 0.8 Ensembl ENCODE 10.9 -82.4 -82402 4.2 SRF ZNF687 NR2F1 BHLHE40 ELF1 DPF2 SP1 IKZF1 NBN HMBOX1 AKAP3 C12orf4 RAD51AP1 LOC103568124 NDUFA9 TIGAR DYRK4
GH12J004613 Promoter 0.5 EPDnew 10.9 -35.5 -35521 0.1 DYRK4 NDUFA9 AKAP3 GC12M004620 ENSG00000272921
GH12J004614 Promoter 0.5 EPDnew 10.9 -35.3 -35348 0.1 DYRK4 AKAP3 NDUFA9 GC12M004620 ENSG00000272921
GH12J004587 Enhancer 0.3 ENCODE 10.7 -61.8 -61765 0.2 CTCF RAD51AP1 C12orf4 DYRK4 GALNT8 GAU1 NDUFA9 AKAP3 LOC103568124
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NDUFA9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NDUFA9 gene promoter:
  • STAT5A
  • PPAR-gamma2
  • PPAR-gamma1
  • HNF-3beta
  • GATA-3
  • FOXO1a
  • FOXO1
  • AML1a
  • Arnt
  • POU6F1 (c2)

Genomic Locations for NDUFA9 Gene

Genomic Locations for NDUFA9 Gene
45,223 bases
Plus strand
40,194 bases
Plus strand

Genomic View for NDUFA9 Gene

Genes around NDUFA9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NDUFA9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NDUFA9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NDUFA9 Gene

Proteins for NDUFA9 Gene

  • Protein details for NDUFA9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • Q14076
    • Q2NKX0

    Protein attributes for NDUFA9 Gene

    377 amino acids
    Molecular mass:
    42510 Da
    Name=FAD; Xref=ChEBI:CHEBI:57692;
    Quaternary structure:
    • Complex I is composed of 45 different subunits. This a component of the hydrophobic protein fraction (PubMed:12611891, PubMed:27626371). Interacts with BLOC1S1 (PubMed:22309213). Interacts with SLC2A4 (By similarity). Interacts with CLOCK (PubMed:28985504).
    • Sequence=CAA54099.1; Type=Frameshift; Positions=18; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NDUFA9 Gene

neXtProt entry for NDUFA9 Gene

Post-translational modifications for NDUFA9 Gene

  • Acetylated on lysine residues. BLOC1S1 is required for acetylation (PubMed:22309213). Acetylated by CLOCK in a circadian manner (PubMed:28985504).
  • Ubiquitination at isoforms=234 and Lys137
  • Modification sites at PhosphoSitePlus

Other Protein References for NDUFA9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NDUFA9 Gene

Domains & Families for NDUFA9 Gene

Gene Families for NDUFA9 Gene

Protein Domains for NDUFA9 Gene

Suggested Antigen Peptide Sequences for NDUFA9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the complex I NDUFA9 subunit family.
  • Belongs to the complex I NDUFA9 subunit family.
genes like me logo Genes that share domains with NDUFA9: view

Function for NDUFA9 Gene

Molecular function for NDUFA9 Gene

UniProtKB/Swiss-Prot Function:
Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.
GENATLAS Biochemistry:
NADH ubiquinone oxidoreductase (Q reductase),component of the complex I multi-subunit enzyme of the oxidative phosphorylation (OXPHOS),iron sulfur-protein 2-like,inner mitochondrial membrane,homolog to 39kDa bovine subunit

Phenotypes From GWAS Catalog for NDUFA9 Gene

Gene Ontology (GO) - Molecular Function for NDUFA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003954 NADH dehydrogenase activity NAS 8486360
GO:0005515 protein binding IPI 19103604
GO:0008137 NADH dehydrogenase (ubiquinone) activity NAS 8486360
GO:0044877 protein-containing complex binding IDA 23209302
GO:0050662 coenzyme binding IEA --
genes like me logo Genes that share ontologies with NDUFA9: view
genes like me logo Genes that share phenotypes with NDUFA9: view

Human Phenotype Ontology for NDUFA9 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for NDUFA9 Gene

Localization for NDUFA9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NDUFA9 Gene

Mitochondrion matrix.

Subcellular locations from

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 NDUFA9 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (3)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NDUFA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus HDA 21630459
GO:0005654 nucleoplasm IDA --
GO:0005739 mitochondrion IEA,IDA --
GO:0005747 mitochondrial respiratory chain complex I IDA 9878551
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with NDUFA9: view

Pathways & Interactions for NDUFA9 Gene

genes like me logo Genes that share pathways with NDUFA9: view

Gene Ontology (GO) - Biological Process for NDUFA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006120 mitochondrial electron transport, NADH to ubiquinone TAS --
GO:0006814 sodium ion transport NAS 8486360
GO:0007623 circadian rhythm IDA 28985504
GO:0032981 mitochondrial respiratory chain complex I assembly TAS --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with NDUFA9: view

No data available for SIGNOR curated interactions for NDUFA9 Gene

Drugs & Compounds for NDUFA9 Gene

(5) Drugs for NDUFA9 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
FAD Approved Pharma Target, cofactor 0
NADH Approved Nutra Target 0
Ubiquinone-1 Experimental Pharma 0
Ubiquinone-2 Experimental Pharma 0
NAD Pharma Full agonist, Agonist, Activator 0

(3) Additional Compounds for NDUFA9 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • FE (II) ion
  • Fe(II)
  • Fe(2+)
  • Ferrous ion
  • Iron ion(2+)
  • CoQH2
  • Coenzymes QH2
  • Reduced ubiquinone
  • Ubiquinol
  • Ubiquinone-1
  • S(2-)
  • Sulphide
  • Sulfanediide
  • Sulfur
genes like me logo Genes that share compounds with NDUFA9: view

Transcripts for NDUFA9 Gene

mRNA/cDNA for NDUFA9 Gene

Unigene Clusters for NDUFA9 Gene

NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NDUFA9 Gene

No ASD Table

Relevant External Links for NDUFA9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NDUFA9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NDUFA9 Gene

mRNA differential expression in normal tissues according to GTEx for NDUFA9 Gene

This gene is overexpressed in Heart - Left Ventricle (x4.8).

Protein differential expression in normal tissues from HIPED for NDUFA9 Gene

This gene is overexpressed in Nasal epithelium (14.4) and Heart (10.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NDUFA9 Gene

Protein tissue co-expression partners for NDUFA9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NDUFA9 Gene:


SOURCE GeneReport for Unigene cluster for NDUFA9 Gene:


Evidence on tissue expression from TISSUES for NDUFA9 Gene

  • Liver(4.6)
  • Muscle(4.6)
  • Intestine(4.5)
  • Blood(4.3)
  • Nervous system(4.1)
  • Lung(3.2)
  • Kidney(2.7)
  • Skin(2.5)
  • Heart(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NDUFA9 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cranial nerve
  • eye
  • eyelid
  • face
  • head
  • meninges
  • neck
  • lung
  • liver
  • hair
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with NDUFA9: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for NDUFA9 Gene

Orthologs for NDUFA9 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NDUFA9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NDUFA9 34 33
  • 99.29 (n)
(Canis familiaris)
Mammalia NDUFA9 33
  • 87.68 (n)
-- 34
  • 85 (a)
(Bos Taurus)
Mammalia NDUFA9 34 33
  • 82.67 (n)
(Mus musculus)
Mammalia Ndufa9 16 34 33
  • 79.34 (n)
(Rattus norvegicus)
Mammalia Ndufa9 33
  • 78.72 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 74 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 73 (a)
-- 34
  • 71 (a)
(Gallus gallus)
Aves NDUFA9 34 33
  • 71.81 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 67 (a)
-- 34
  • 63 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ndufa9 33
  • 67.2 (n)
Str.8681 33
African clawed frog
(Xenopus laevis)
Amphibia MGC64316 33
(Danio rerio)
Actinopterygii si:ch211-251f6.5 34 33
  • 67.85 (n)
ndufa9 34
  • 61 (a)
wufc41f12 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.672 33
fruit fly
(Drosophila melanogaster)
Insecta CG6020 34 35 33
  • 50 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010792 33
  • 49 (n)
(Caenorhabditis elegans)
Secernentea Y53G8AL.2 34 35 33
  • 49.12 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G20360 33
  • 55.93 (n)
(Oryza sativa)
Liliopsida Os02g0816800 33
  • 53.84 (n)
Os.10342 33
(Zea mays)
Liliopsida Zm.8933 33
(Triticum aestivum)
Liliopsida Ta.5022 33
bread mold
(Neurospora crassa)
Ascomycetes NCU02373 33
  • 45.05 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8552 34
  • 29 (a)
Species where no ortholog for NDUFA9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • 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)
  • 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)

Evolution for NDUFA9 Gene

Gene Tree for NDUFA9 (if available)
Gene Tree for NDUFA9 (if available)
Evolutionary constrained regions (ECRs) for NDUFA9: view image

Paralogs for NDUFA9 Gene

Paralogs for NDUFA9 Gene Pseudogenes for NDUFA9 Gene

genes like me logo Genes that share paralogs with NDUFA9: view

Variants for NDUFA9 Gene

Sequence variations from dbSNP and Humsavar for NDUFA9 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs199592341 pathogenic, Leigh syndrome due to mitochondrial complex I deficiency, Leigh syndrome (LS) [MIM:256000] 4,685,324(+) G/A/C/T coding_sequence_variant, missense_variant
rs35263902 likely-pathogenic, uncertain-significance, not provided, not specified 4,654,828(+) G/A/T coding_sequence_variant, missense_variant
rs71579253 uncertain-significance, not specified, not provided 4,654,857(+) C/T coding_sequence_variant, missense_variant
rs768333416 likely-pathogenic, not provided 4,662,640(+) G/A intron_variant
rs1057521037 likely-benign, not specified 4,669,812(+) C/T coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for NDUFA9 Gene

Variant ID Type Subtype PubMed ID
nsv1036308 CNV loss 25217958
nsv1040098 CNV gain 25217958
nsv483060 CNV loss 15286789
nsv557125 CNV loss 21841781
nsv557126 CNV loss 21841781
nsv587 CNV insertion 18451855
nsv832318 CNV gain 17160897

Variation tolerance for NDUFA9 Gene

Residual Variation Intolerance Score: 80.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.74; 46.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NDUFA9 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NDUFA9 Gene

Disorders for NDUFA9 Gene

MalaCards: The human disease database

(4) MalaCards diseases for NDUFA9 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
leigh syndrome
  • ls
leigh syndrome with leukodystrophy
  • infantile subacute necrotizing encephalopathy with leukodystrophy
listeria meningitis
  • meningitis, listeria
  • infection by listeria monocytogenes
- elite association - COSMIC cancer census association via MalaCards


  • Leigh syndrome (LS) [MIM:256000]: An early-onset progressive neurodegenerative disorder characterized by the presence of focal, bilateral lesions in one or more areas of the central nervous system including the brainstem, thalamus, basal ganglia, cerebellum and spinal cord. Clinical features depend on which areas of the central nervous system are involved and include subacute onset of psychomotor retardation, hypotonia, ataxia, weakness, vision loss, eye movement abnormalities, seizures, and dysphagia. {ECO:0000269 PubMed:22114105}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for NDUFA9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NDUFA9: view

No data available for Genatlas for NDUFA9 Gene

Publications for NDUFA9 Gene

  1. Construction and evaluation of a hncDNA library of human 12p transcribed sequences derived from a somatic cell hybrid. (PMID: 8486360) Baens M … Marynen P (Genomics 1993) 2 3 4 58
  2. CLOCK Acetylates ASS1 to Drive Circadian Rhythm of Ureagenesis. (PMID: 28985504) Lin R … Guan KL (Molecular cell 2017) 3 4 58
  3. Accessory subunits are integral for assembly and function of human mitochondrial complex I. (PMID: 27626371) Stroud DA … Ryan MT (Nature 2016) 3 4 58
  4. Identification of a molecular component of the mitochondrial acetyltransferase programme: a novel role for GCN5L1. (PMID: 22309213) Scott I … Sack MN (The Biochemical journal 2012) 3 4 58
  5. Defective NDUFA9 as a novel cause of neonatally fatal complex I disease. (PMID: 22114105) van den Bosch BJ … Smeets HJ (Journal of medical genetics 2012) 3 4 58

Products for NDUFA9 Gene

Sources for NDUFA9 Gene

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