NDUFS2

gene
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Also known as CI-49

Summary

NDUFS2 (NADH:ubiquinone oxidoreductase core subunit S2, HGNC:7708) is a protein-coding gene on chromosome 1q23.3, encoding NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (O75306). Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. It is a selective cancer dependency (DepMap: 40.6% of cell lines).

The protein encoded by this gene is a core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (complex I). Mammalian mitochondrial complex I is composed of at least 43 different subunits, 7 of which are encoded by the mitochondrial genome, and the rest are the products of nuclear genes. The iron-sulfur protein fraction of complex I is made up of 7 subunits, including this gene product. Complex I catalyzes the NADH oxidation with concomitant ubiquinone reduction and proton ejection out of the mitochondria. Mutations in this gene are associated with mitochondrial complex I deficiency. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 4720 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): mitochondrial disease (Definitive, ClinGen) — +6 more curated relationships
  • GWAS associations: 8
  • Clinical variants (ClinVar): 254 total — 6 pathogenic, 6 likely-pathogenic
  • Phenotypes (HPO): 78
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 40.6% of screened cell lines
  • MANE Select transcript: NM_001377299

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:7708
Approved symbolNDUFS2
NameNADH:ubiquinone oxidoreductase core subunit S2
Location1q23.3
Locus typegene with protein product
StatusApproved
AliasesCI-49
Ensembl geneENSG00000158864
Ensembl biotypeprotein_coding
OMIM602985
Entrez4720

Gene structure

Transcript identifiers

Ensembl transcripts: 93 — 40 retained_intron, 23 nonsense_mediated_decay, 18 protein_coding, 12 protein_coding_CDS_not_defined

ENST00000367993, ENST00000392179, ENST00000465923, ENST00000467295, ENST00000468828, ENST00000473321, ENST00000475570, ENST00000478866, ENST00000479948, ENST00000480762, ENST00000483804, ENST00000492153, ENST00000493849, ENST00000496133, ENST00000496553, ENST00000676535, ENST00000676583, ENST00000676600, ENST00000676653, ENST00000676726, ENST00000676770, ENST00000676795, ENST00000676871, ENST00000676972, ENST00000676991, ENST00000677033, ENST00000677045, ENST00000677050, ENST00000677063, ENST00000677081, ENST00000677089, ENST00000677103, ENST00000677138, ENST00000677178, ENST00000677231, ENST00000677336, ENST00000677350, ENST00000677358, ENST00000677383, ENST00000677453, ENST00000677457, ENST00000677471, ENST00000677495, ENST00000677547, ENST00000677550, ENST00000677577, ENST00000677579, ENST00000677613, ENST00000677643, ENST00000677653, ENST00000677657, ENST00000677736, ENST00000677745, ENST00000677807, ENST00000677809, ENST00000677837, ENST00000677846, ENST00000677916, ENST00000677925, ENST00000677948, ENST00000678052, ENST00000678068, ENST00000678130, ENST00000678328, ENST00000678356, ENST00000678484, ENST00000678492, ENST00000678507, ENST00000678511, ENST00000678532, ENST00000678559, ENST00000678605, ENST00000678613, ENST00000678648, ENST00000678783, ENST00000678793, ENST00000678850, ENST00000678880, ENST00000678911, ENST00000678966, ENST00000678982, ENST00000679064, ENST00000679071, ENST00000679142, ENST00000679169, ENST00000679176, ENST00000679215, ENST00000679218, ENST00000679239, ENST00000679282, ENST00000873085, ENST00000960014, ENST00000960015

RefSeq mRNA: 8 — MANE Select: NM_001377299 NM_001166159, NM_001377298, NM_001377299, NM_001377300, NM_001377301, NM_001377302, NM_001410889, NM_004550

CCDS: CCDS1224, CCDS53404, CCDS91086

Canonical transcript exons

ENST00000676972 — 14 exons

ExonStartEnd
ENSE00001884216161214156161214395
ENSE00003464463161203437161203543
ENSE00003465746161213649161213732
ENSE00003466143161210111161210188
ENSE00003471424161213864161213921
ENSE00003489152161206407161206597
ENSE00003495523161209857161209931
ENSE00003541082161213380161213475
ENSE00003550227161209193161209313
ENSE00003567087161212351161212480
ENSE00003587080161210591161210710
ENSE00003634980161210304161210389
ENSE00003672735161209483161209595
ENSE00003906071161202367161202480

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 99.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 75.9535 / max 561.1559, expressed in 1824 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
621775.47561824
62160.4779298

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209899.19gold quality
gastrocnemiusUBERON:000138899.01gold quality
heart left ventricleUBERON:000208498.98gold quality
cardiac ventricleUBERON:000208298.96gold quality
mucosa of transverse colonUBERON:000499198.84gold quality
muscle of legUBERON:000138398.81gold quality
right adrenal glandUBERON:000123398.75gold quality
heart right ventricleUBERON:000208098.70gold quality
right adrenal gland cortexUBERON:003582798.70gold quality
right atrium auricular regionUBERON:000663198.69gold quality
left ventricle myocardiumUBERON:000656698.66gold quality
muscle organUBERON:000163098.62gold quality
hindlimb stylopod muscleUBERON:000425298.60gold quality
cardiac atriumUBERON:000208198.59gold quality
left adrenal glandUBERON:000123498.51gold quality
heartUBERON:000094898.47gold quality
body of tongueUBERON:001187698.37gold quality
left adrenal gland cortexUBERON:003582598.36gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451198.30gold quality
diaphragmUBERON:000110398.24gold quality
skeletal muscle tissueUBERON:000113498.21gold quality
adrenal cortexUBERON:000123598.20gold quality
vastus lateralisUBERON:000137998.20gold quality
deltoidUBERON:000147698.17gold quality
left ovaryUBERON:000211998.15gold quality
right hemisphere of cerebellumUBERON:001489098.15gold quality
transverse colonUBERON:000115798.14gold quality
quadriceps femorisUBERON:000137798.12gold quality
adrenal glandUBERON:000236998.10gold quality
right ovaryUBERON:000211898.09gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-6379no808.30
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting NDUFS2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-8485100.0077.574731
HSA-MIR-4735-5P99.4368.491780
HSA-MIR-94099.3766.142064
HSA-MIR-6808-5P99.3166.232150
HSA-MIR-6893-5P99.3166.252119
HSA-MIR-427999.1966.702437
HSA-MIR-2277-3P91.9462.27299

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 40.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

  • Trx, dCBP, and Sbf1 are closely linked, physically and functionally, in the maintenance of Hox gene expression. (PMID:11701926)
  • The Drosophila trithorax protein is a coactivator required to prevent re-establishment of polycomb silencing. (PMID:11973279)
  • Genomic imprinting in Drosophila is maintained by the products of Suppressor of variegation and trithorax group, but not Polycomb group, genes. (PMID:12242505)
  • Trithorax interacts with type 1 serine/threonine protein phosphatase. (PMID:12524522)
  • This suggests that TRITHORAX bound to certain regulatory chromosome regions interacts with the adjacent elements of the nuclear scaffold, i.e., links the regions of actively transcribed genes with the nuclear matrix. (PMID:12669422)
  • identified several members of the Polycomb and trithorax classes of genes required for the normal pattern of photoreceptor differentiation (PMID:15020417)
  • Results suggest that protein phosphatase 1beta9C and Trithorax cooperate in Drosophila wing development. (PMID:15366010)
  • Deletion analysis showed that the C-terminus of dDYRK2 modulated the interaction with SNR1 and TRX. (PMID:16671894)
  • it is proposed that that the Trithorax complex, TAC1, promotes the mosaic pattern of Ubx expression by facilitating transcriptional elongation of bxd noncoding RNAs, which represses Ubx transcription (PMID:17174895)
  • Data demonstrate that the Drosophila homologs of mixed-lineage leukemia protein and host cell factor 1, called Trithorax and dHCF, are both cleaved by Drosophila taspase 1. (PMID:17698583)
  • Computational analysis ofmicroarray data, identified 25 clusters of genes potentially regulated by TRX; most of these clusters consist of genes that encode structural proteins involved in cuticle formation. (PMID:18783608)
  • results indicate that DNA binding proteins serve as platforms to assist PcG and trxG binding. Furthermore, several DNA sequence features discriminate between PcG- and TRX-N-bound regions (PMID:19143474)
  • Hsp90 cooperates with Trx at chromatin for maintaining the active expression state of targets like the Hox genes. (PMID:19144915)
  • These findings establish a role for PRC2 and TRX in the modulation of organismal longevity and stress resistance and indicate that moderate perturbation of Polycomb silencing can increase longevity. (PMID:20018689)
  • Polycomb and trithorax control genome expression by determining the alternative epigenetic states of chromatin for key developmental regulators (PMID:21254568)
  • dHCF possesses Enhancer of TrxG and PcG (ETP) properties. (PMID:22174740)
  • Data imply that Trx, Pc, and E(z) remain bound or rapidly rebind to nascent DNA in the absence of trimethylated histones during DNA replication in Drosophila embryos. (PMID:22921915)
  • mutations in PcG components and in TrxG members found in chromatin remodeling complexes enhance the gcm dominant phenotype, suggesting a balanced action of these chromatin modifiers regulate Gcm function (PMID:23300465)
  • CpG island encompassing the promoter and first exon of human DNMT3L gene is a PcG/TrX response element (PMID:24743422)
  • From the Drosophila melanogaster vestigial (vg) Polycomb response element/Trithorax response element switches the status of the element. (PMID:25108384)
  • Trithorax maintains the functional heterogeneity of neural stem cells through the transcription factor buttonhead. (PMID:25285447)
  • Trithorax has a role in regulating systemic signaling during Drosophila imaginal disc regeneration (PMID:26487779)
  • If ASH1 or TRX function is lost or reduced, heterochromatin can spread into these domains creating a sink that diverts heterochromatic proteins from other variegating locations, which then may express a suppressed phenotype. (PMID:27373142)
  • Trithorax positively regulates gene expression in Drosophila and co-occupies PREs to antagonize Polycomb-dependent silencing. Trx-dependent H3K4 dimethylation (H3K4me2) marks Drosophila PREs and maintains the developmental expression pattern of nearby genes. (PMID:27447986)
  • Taken together, these data indicate that Atrophin is a major Trithorax-like cofactor that functions to moderate developmental gene transcription. (PMID:28327288)
  • Mrg15 is a subunit of the Ash1 complex, a stimulator of Ash1 enzymatic activity and a critical regulator of the TrxG protein function of Ash1 in Drosophila. (PMID:29158494)
  • Control of the gene activity by polycomb and trithorax group proteins in Drosophila (PMID:29372960)
  • we demonstrate that the evolutionary conserved Lim3 core promoter provides basic Lim3 expression, whereas structural changes in the Lim3 PRE of distal promoter provide stage-, and tissue-specific Lim3 expression. Therefore, we hypothesize that PcG/TrxG proteins, which are directly involved in Lim3 transcription regulation, participate in lifespan control. (PMID:29555581)
  • Trx and Grx have both, common and specific protein Cys redox targets and that down regulation of either redoxin has markedly different metabolic outcomes. They reflect the delicate sensitivity of redox equilibrium to changes in any of the elements involved and the difficulty of forecasting metabolic responses to redox environmental changes. (PMID:30639960)
  • Trx, Ash1, and CBP proteins are required for the correct chromosome segregation and that Ash1 and CBP mediate for Cid/CENP-A recruitment at centromeres through post-translational histone modifications. (PMID:31203392)
  • Dynamic Competition of Polycomb and Trithorax in Transcriptional Programming. (PMID:31928411)
  • Distinct Roles for COMPASS Core Subunits Set1, Trx, and Trr in the Epigenetic Regulation of Drosophila Heart Development. (PMID:38139143)
  • Our results confirm that NDUFS2 is a mutational hotspot in Caucasian children with isolated complex I deficiency and recommend the routine diagnostic investigation of this gene in patients with Leigh or Leigh-like phenotypes. (PMID:20819849)
  • The NDUFS2 mutation affects complex I enzymatic function. (PMID:22036843)
  • study describes clinical, radiological, biochemical and molecular data of 6 patients with Leigh syndrome with novel mutations in NDUFV1 and NDUFS2; 2 siblings were compound heterozygotes for an undescribed E104A mutation in NDUFS2 (PMID:23266820)
  • NDUFAF7 methylates arginine 85 in the NDUFS2 subunit of human complex I. (PMID:24089531)
  • Results found nominal significant associations of 2 SNPs in the NDUFS1 gene and 4 SNPs in the NDUFS2 gene with early onset schizophrenia (EOS), but none of these associations survived the Bonferroni correction. (PMID:26053550)
  • compound heterozygosity for severe and hypomorphic NDUFS2 mutations can cause non-syndromic hereditary optic neuropathy. (PMID:28031252)
  • findings uncover a novel S100A4 function and highlight its importance in controlling NDUFS2 expression to regulate the plasticity of mitochondrial metabolism and thereby promote the invasive and metastatic capacity in lung cancer (PMID:30885944)
  • Complex I protein NDUFS2 is vital for growth, ROS generation, membrane integrity, apoptosis, and mitochondrial energetics. (PMID:33744462)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriondufs2ENSDARG00000007526
mus_musculusNdufs2ENSMUSG00000013593
rattus_norvegicusNdufs2ENSRNOG00000038372
drosophila_melanogasterND-49LFBGN0039331
drosophila_melanogasterND-49FBGN0039909
caenorhabditis_elegansWBGENE00001520
caenorhabditis_elegansWBGENE00006463

Protein

Protein identifiers

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialO75306 (reviewed: O75306)

Alternative names: Complex I-49kD, NADH-ubiquinone oxidoreductase 49 kDa subunit

All UniProt accessions (18): O75306, A0A7I2V2B9, A0A7I2V2P1, A0A7I2V3J6, A0A7I2V410, A0A7I2V4G5, A0A7I2V4W5, A0A7I2V4X8, A0A7I2V517, A0A7I2V596, A0A7I2V5D5, A0A7I2V5E2, A0A7I2V5G4, A0A7I2V5X7, A0A7I2V630, A0A7I2YQD8, A0A7I2YQG7, A0A7I2YQX7

UniProt curated annotations — full annotation on UniProt →

Function. Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity of complex I. Essential for the assembly of complex I. Redox-sensitive, critical component of the oxygen-sensing pathway in the pulmonary vasculature which plays a key role in acute pulmonary oxygen-sensing and hypoxic pulmonary vasoconstriction. Plays an important role in carotid body sensing of hypoxia. Essential for glia-like neural stem and progenitor cell proliferation, differentiation and subsequent oligodendrocyte or neuronal maturation.

Subunit / interactions. Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Component of the iron-sulfur (IP) fragment of the enzyme. Interacts with NDUFAF3. Interacts with NDUFAF7. Interacts with CERS2.

Subcellular location. Mitochondrion inner membrane.

Post-translational modifications. Dimethylation at Arg-118 by NDUFAF7 takes place after NDUFS2 assembles into the complex I, leading to stabilize the early intermediate complex.

Disease relevance. Mitochondrial complex I deficiency, nuclear type 6 (MC1DN6) [MIM:618228] A form of mitochondrial complex I deficiency, the most common biochemical signature of mitochondrial disorders, a group of highly heterogeneous conditions characterized by defective oxidative phosphorylation, which collectively affects 1 in 5-10000 live births. Clinical disorders have variable severity, ranging from lethal neonatal disease to adult-onset neurodegenerative disorders. Phenotypes include macrocephaly with progressive leukodystrophy, non-specific encephalopathy, cardiomyopathy, myopathy, liver disease, Leigh syndrome, Leber hereditary optic neuropathy, and some forms of Parkinson disease. MC1DN6 transmission pattern is consistent with autosomal recessive inheritance. The disease is caused by variants affecting the gene represented in this entry. Leber-like hereditary optic neuropathy, autosomal recessive 2 (LHONAR2) [MIM:620569] An autosomal recessive form of Leber hereditary optic neuropathy, a mitochondrial disease resulting in bilateral painless loss of central vision due to selective degeneration of the retinal ganglion cells and their axons. LHONAR2 is characterized by subacute bilateral or asymmetrical visual loss, optic nerve pseudoedema and peripapillary telangiectasia in the early phase of the disease, and eventual partial recovery in some patients. The disease is caused by variants affecting the gene represented in this entry.

Cofactor. Binds 1 [4Fe-4S] cluster.

Similarity. Belongs to the complex I 49 kDa subunit family.

Isoforms (2)

UniProt IDNamesCanonical?
O75306-11yes
O75306-22

RefSeq proteins (8): NP_001159631, NP_001364227, NP_001364228, NP_001364229, NP_001364230, NP_001364231, NP_001397818, NP_004541 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001135NADH_Q_OxRdtase_suDDomain
IPR014029NADH_UbQ_OxRdtase_49kDa_CSConserved_site
IPR022885NDH1_su_D/HFamily
IPR029014NiFe-Hase_largeHomologous_superfamily

Pfam: PF00346

Catalyzed reactions (Rhea), 1 shown:

  • a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) (RHEA:29091)

UniProt features (53 total): helix 18, strand 11, sequence variant 10, turn 5, binding site 3, modified residue 2, transit peptide 1, chain 1, sequence conflict 1, splice variant 1

Structure

Experimental structures (PDB)

8 structures.

PDBMethodResolution (Å)
9I4IELECTRON MICROSCOPY2.63
9TI4ELECTRON MICROSCOPY2.66
5XTBELECTRON MICROSCOPY3.4
9CWTELECTRON MICROSCOPY3.44
5XTCELECTRON MICROSCOPY3.7
5XTDELECTRON MICROSCOPY3.7
5XTHELECTRON MICROSCOPY3.9
5XTIELECTRON MICROSCOPY17.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O75306-F189.620.81

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (3): 326; 332; 347

Post-translational modifications (2): 62, 118

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-611105Respiratory electron transport
R-HSA-6799198Complex I biogenesis
R-HSA-1428517Aerobic respiration and respiratory electron transport
R-HSA-1430728Metabolism

MSigDB gene sets: 431 (showing top): MODULE_93, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, MODY_HIPPOCAMPUS_POSTNATAL, MODULE_77, LFA1_Q6, MORF_HDAC1, GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY, GOBP_NEUROGENESIS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_NUCLEOSIDE_PHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_NEURAL_PRECURSOR_CELL_PROLIFERATION

GO Biological Process (10): mitochondrial electron transport, NADH to ubiquinone (GO:0006120), aerobic respiration (GO:0009060), neurogenesis (GO:0022008), mitochondrial respiratory chain complex I assembly (GO:0032981), gliogenesis (GO:0042063), mitochondrial ATP synthesis coupled electron transport (GO:0042775), proton motive force-driven mitochondrial ATP synthesis (GO:0042776), neural precursor cell proliferation (GO:0061351), cellular response to oxygen levels (GO:0071453), proton transmembrane transport (GO:1902600)

GO Molecular Function (13): NADH dehydrogenase (ubiquinone) activity (GO:0008137), electron transfer activity (GO:0009055), oxidoreductase activity, acting on NAD(P)H (GO:0016651), oxygen sensor activity (GO:0019826), ubiquitin protein ligase binding (GO:0031625), metal ion binding (GO:0046872), quinone binding (GO:0048038), NAD binding (GO:0051287), 4 iron, 4 sulfur cluster binding (GO:0051539), NADH dehydrogenase activity (GO:0003954), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), iron-sulfur cluster binding (GO:0051536)

GO Cellular Component (5): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial matrix (GO:0005759), respiratory chain complex I (GO:0045271), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Aerobic respiration and respiratory electron transport1
Respiratory electron transport1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
mitochondrion3
aerobic electron transport chain1
mitochondrial ATP synthesis coupled electron transport1
cellular respiration1
nervous system development1
cell differentiation1
NADH dehydrogenase complex assembly1
mitochondrial respiratory chain complex assembly1
neurogenesis1
ATP synthesis coupled electron transport1
oxidative phosphorylation1
proton motive force-driven ATP synthesis1
cell population proliferation1
response to oxygen levels1
cellular response to chemical stimulus1
monoatomic cation transmembrane transport1
NADH dehydrogenase activity1
electron transfer activity1
proton transmembrane transporter activity1
oxidoreduction-driven active transmembrane transporter activity1
oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor1
active monoatomic ion transmembrane transporter activity1
molecular_function1
oxidoreductase activity1
oxygen binding1
molecular sensor activity1
ubiquitin-like protein ligase binding1
cation binding1
small molecule binding1
adenyl nucleotide binding1
iron-sulfur cluster binding1
oxidoreductase activity, acting on NAD(P)H1
binding1
catalytic activity1
metal cluster binding1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
intracellular organelle lumen1

Protein interactions and networks

STRING

3815 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NDUFS2NDUFS3O75489999
NDUFS2NDUFS7O75251998
NDUFS2NDUFS8O00217998
NDUFS2NDUFS1P28331998
NDUFS2NDUFV1P49821996
NDUFS2NDUFV2P19404993
NDUFS2NDUFA5Q16718971
NDUFS2NDUFS6O75380964
NDUFS2NDUFS4O43181956
NDUFS2NDUFA9Q16795914
NDUFS2NDUFA10O95299905
NDUFS2NDUFAF4Q9P032879
NDUFS2MT-ND1P03886870
NDUFS2NDUFA11Q86Y39869
NDUFS2NDUFS5O43920858

IntAct

185 interactions, top by confidence:

ABTypeScore
NDUFS3NDUFS2psi-mi:“MI:0914”(association)0.850
NDUFS2NDUFS3psi-mi:“MI:0914”(association)0.850
NDUFS3NDUFS2psi-mi:“MI:0915”(physical association)0.850
NDUFS2NDUFS3psi-mi:“MI:0915”(physical association)0.850
NDUFA9NDUFS2psi-mi:“MI:0915”(physical association)0.740
NDUFS3NDUFS8psi-mi:“MI:0914”(association)0.730
NDUFV2NDUFS2psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
HSPD1NUDT19psi-mi:“MI:0914”(association)0.710
NDUFS7NDUFS8psi-mi:“MI:0914”(association)0.640
NDUFS6NDUFS8psi-mi:“MI:0914”(association)0.640
NDUFAF4NDUFS8psi-mi:“MI:0914”(association)0.640
NDUFA13NDUFS8psi-mi:“MI:0914”(association)0.640
NDUFA9NDUFS4psi-mi:“MI:0914”(association)0.640

BioGRID (412): NDUFS2 (Affinity Capture-RNA), NDUFS2 (Affinity Capture-RNA), NDUFS2 (Affinity Capture-RNA), NDUFS2 (Affinity Capture-MS), NDUFS2 (Affinity Capture-MS), NDUFS2 (Affinity Capture-MS), NDUFS2 (Affinity Capture-MS), NDUFS2 (Affinity Capture-MS), DLD (Co-fractionation), LMAN2 (Co-fractionation), NDUFS1 (Co-fractionation), NDUFS2 (Co-fractionation), NDUFS2 (Co-fractionation), NDUFS2 (Co-fractionation), NDUFS2 (Co-fractionation)

ESM2 similar proteins: A0QJV0, A0QU33, A1BF35, A2CD94, A4FPT8, A4SF45, A5FX11, A5GP75, A5GWA1, A5VAM0, A5VPY6, A6X1N0, A9B4Z7, A9MAI2, B0CLD2, B0SZ49, B1ZRT0, B2S546, B3PW00, B4RCM6, B5ZYL5, B6JGW3, O75306, P17694, P22142, Q0I6T6, Q0MQG3, Q0MQG4, Q0MQG5, Q135X7, Q1GTK0, Q1MIL2, Q28T72, Q2G5Y6, Q2K9T1, Q2NA64, Q2YNG0, Q31ME6, Q3AGW8, Q3AVZ9

Diamond homologs: A0LDS4, A0LRI4, A0PR41, A0QJV0, A0QU33, A1K5B1, A1KNE4, A1SE30, A1T6A3, A1TLL9, A1UDA1, A1W4M5, A2SFM9, A3PWR8, A4FPT8, A4TDA8, A4XC35, A5CES2, A5FX11, A5G9B6, A5U7G4, A5UZH7, A6UFK4, A7NIV9, A8EZ86, A8F1C5, A8GN50, A8GRR5, A8GX80, A8LC98, A8M619, A9B4Z7, A9BNB1, A9CJA9, A9HRT9, A9WFB4, B0BX71, B0ULK7, B1MPG7, B1W516

SIGNOR signaling

3 interactions.

AEffectBMechanism
NDUFS2“form complex”“NADH-ubiquinone oxidoreductase-Mitochondrial respiratory chain complex I”binding
CDK1“up-regulates activity”NDUFS2phosphorylation
CyclinB/CDK1“up-regulates activity”NDUFS2phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 144 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Complex I biogenesis2948.0×2e-40
Respiratory electron transport3028.6×3e-34
Aerobic respiration and respiratory electron transport3026.6×2e-33
Mitochondrial protein degradation1011.4×1e-06

GO biological processes:

GO termPartnersFoldFDR
mitochondrial electron transport, NADH to ubiquinone2161.7×9e-31
proton motive force-driven mitochondrial ATP synthesis2349.6×7e-31
mitochondrial respiratory chain complex I assembly1447.2×3e-18
aerobic respiration2346.7×1e-30

Disease & clinical

Clinical variants and AI predictions

ClinVar

254 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic6
Likely pathogenic6
Uncertain significance109
Likely benign72
Benign16

Top pathogenic / likely-pathogenic (12)

Variant IDHGVSClassification
1451468NM_001377299.1(NDUFS2):c.128G>A (p.Trp43Ter)Pathogenic
2627943NM_001377299.1(NDUFS2):c.923A>G (p.Tyr308Cys)Pathogenic
4312718NM_001377299.1(NDUFS2):c.1102C>T (p.Arg368Ter)Pathogenic
4714351NM_001377299.1(NDUFS2):c.90del (p.Ser31fs)Pathogenic
6710NM_001377299.1(NDUFS2):c.686C>A (p.Pro229Gln)Pathogenic
872511NM_001377299.1(NDUFS2):c.442G>A (p.Glu148Lys)Pathogenic
1324786NM_001377299.1(NDUFS2):c.646C>T (p.Arg216Ter)Likely pathogenic
1478205NM_001377299.1(NDUFS2):c.1212+1G>TLikely pathogenic
2010294NM_001377299.1(NDUFS2):c.867-1G>ALikely pathogenic
4312697NM_001377299.1(NDUFS2):c.805C>T (p.Arg269Ter)Likely pathogenic
522715NM_001377299.1(NDUFS2):c.268G>A (p.Ala90Thr)Likely pathogenic
6711NM_001377299.1(NDUFS2):c.1237T>C (p.Ser413Pro)Likely pathogenic

SpliceAI

1708 predictions. Top by Δscore:

VariantEffectΔscore
1:161206399:C:Gacceptor_gain1.0000
1:161206406:GAT:Gacceptor_gain1.0000
1:161206406:GATGT:Gacceptor_gain1.0000
1:161206525:G:GTdonor_gain1.0000
1:161206560:GCAC:Gdonor_gain1.0000
1:161206567:G:GTdonor_gain1.0000
1:161209188:CCCA:Cacceptor_loss1.0000
1:161209189:CCA:Cacceptor_loss1.0000
1:161209191:A:Cacceptor_loss1.0000
1:161209192:G:GCacceptor_loss1.0000
1:161209472:T:TAacceptor_gain1.0000
1:161209479:ACAGT:Aacceptor_gain1.0000
1:161209480:CA:Cacceptor_loss1.0000
1:161209481:A:AGacceptor_gain1.0000
1:161209481:AGT:Aacceptor_gain1.0000
1:161209482:G:Aacceptor_loss1.0000
1:161209482:G:GGacceptor_gain1.0000
1:161209482:GT:Gacceptor_gain1.0000
1:161209482:GTG:Gacceptor_gain1.0000
1:161209482:GTGC:Gacceptor_gain1.0000
1:161209482:GTGCT:Gacceptor_gain1.0000
1:161209592:GAAG:Gdonor_gain1.0000
1:161209594:AGGTA:Adonor_loss1.0000
1:161209596:GTAAG:Gdonor_loss1.0000
1:161209597:T:Gdonor_loss1.0000
1:161210302:A:AGacceptor_gain1.0000
1:161210303:G:GGacceptor_gain1.0000
1:161210383:GTTT:Gdonor_gain1.0000
1:161210384:TTTT:Tdonor_gain1.0000
1:161210586:CACA:Cacceptor_loss1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000215905 (1:161201143 C>T), RS1000247065 (1:161201522 A>T), RS1000550277 (1:161199368 G>A), RS1000852820 (1:161198252 T>C), RS1000861295 (1:161212740 G>T), RS1000905157 (1:161198500 G>A), RS1000920945 (1:161205384 T>G), RS1000963834 (1:161198002 C>T), RS1000987613 (1:161199714 A>G), RS1001046124 (1:161211509 G>A,C,T), RS1001182443 (1:161196947 C>T), RS1001236405 (1:161197189 C>T), RS1001246555 (1:161202840 A>G), RS1001357326 (1:161195874 A>G), RS1001373653 (1:161203271 C>G,T)

Disease associations

OMIM: gene MIM:602985 | disease phenotypes: MIM:618228, MIM:252010, MIM:620569, MIM:535000

GenCC curated gene-disease

DiseaseClassificationInheritance
mitochondrial complex I deficiency, nuclear type 6DefinitiveAutosomal recessive
Leber hereditary optic neuropathySupportiveMitochondrial
Leigh syndrome with leukodystrophySupportiveAutosomal recessive
mitochondrial complex I deficiencySupportiveAutosomal recessive
Leigh syndrome with cardiomyopathySupportiveAutosomal recessive

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
mitochondrial diseaseDefinitiveAR
Leigh syndromeDefinitiveAR

Mondo (8): mitochondrial complex I deficiency, nuclear type 6 (MONDO:0032611), mitochondrial complex I deficiency, nuclear type 1 (MONDO:0100224), optic atrophy (MONDO:0003608), mitochondrial complex I deficiency (MONDO:0100133), Leber-like hereditary optic neuropathy, autosomal recessive 2 (MONDO:0958197), Leber hereditary optic neuropathy (MONDO:0010788), (MONDO:0016815), Leigh syndrome with cardiomyopathy (MONDO:0019083)

Orphanet (2): Isolated complex I deficiency (Orphanet:2609), Leber hereditary optic neuropathy (Orphanet:104)

HPO phenotypes

78 total (30 of 78 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000114Proximal tubulopathy
HP:0000252Microcephaly
HP:0000407Sensorineural hearing impairment
HP:0000486Strabismus
HP:0000508Ptosis
HP:0000512Abnormal electroretinogram
HP:0000529Progressive visual loss
HP:0000543Optic disc pallor
HP:0000551Color vision defect
HP:0000576Centrocecal scotoma
HP:0000603Central scotoma
HP:0000618Blindness
HP:0000622Blurred vision
HP:0000639Nystagmus
HP:0000642Red-green dyschromatopsia
HP:0000648Optic atrophy
HP:0000649Abnormality of visual evoked potentials
HP:0000666Horizontal nystagmus
HP:0000817Reduced eye contact
HP:0000819Diabetes mellitus
HP:0001138Optic neuropathy
HP:0001251Ataxia
HP:0001252Hypotonia
HP:0001254Lethargy
HP:0001263Global developmental delay
HP:0001270Motor delay
HP:0001290Generalized hypotonia
HP:0001298Encephalopathy
HP:0001324Muscle weakness

GWAS associations

8 associations (top):

StudyTraitp-value
GCST004608_41Granulocyte percentage of myeloid white cells2.000000e-10
GCST005038_11Allergic disease (asthma, hay fever or eczema)1.000000e-11
GCST007797_50Asthma onset (childhood vs adult)1.000000e-06
GCST007798_9Asthma9.000000e-12
GCST007800_18Asthma (childhood onset)3.000000e-32
GCST008916_64Asthma2.000000e-08
GCST009719_20Allergic rhinitis4.000000e-10
GCST009720_86Asthma1.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007997granulocyte percentage of myeloid white cells
EFO:0004847age at onset

MeSH disease descriptors (3)

DescriptorNameTree numbers
D009896Optic AtrophyC10.292.700.225; C11.640.451
D029242Optic Atrophy, Hereditary, LeberC10.292.700.225.500.400; C10.574.500.662.400; C11.270.564.400; C11.640.451.451.400; C16.320.290.564.400; C16.320.400.630.400; C18.452.660.670
C537475Mitochondrial complex I deficiency (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL2363065 (PROTEIN COMPLEX), CHEMBL3039 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

16 potent at pChembl≥5 of 26 total, top 14 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.48IC5033nMCHEMBL4798829
7.34Kd45.26nMCHEMBL3752910
7.34ED5045.26nMCHEMBL3752910
7.10IC5079nMCHEMBL4798829
6.06IC50870nMR-(+)-MARMIN-6’-UNDECANOATE
6.04IC50920nMR-(+)-MARMIN-6’-LINOLEATE
5.91Kd1236nMCHEMBL5653589
5.91ED501236nMCHEMBL5653589
5.63IC502350nMR-(+)-MARMIN-6’-LINOLEATE
5.51IC503080nMR-(+)-MARMIN-6’-OCTANOATE
5.43IC503670nMR-(+)-MARMIN-6’-UNDECANOATE
5.43IC503710nMR-(+)-MARMIN-6’-OCTANOATE
5.31IC504900nM(+)-9’-ISOVALEROXYLARICIRESINOL
5.04IC509100nM(+)-9’-ISOVALEROXYLARICIRESINOL

PubChem BioAssay actives

10 with measured affinity, of 32 total; 6 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148853: Binding affinity to human NDUFS2 incubated for 45 mins by Kinobead based pull down assaykd0.0453uM
[(E,3R)-2-hydroxy-2,6-dimethyl-8-(2-oxochromen-7-yl)oxyoct-6-en-3-yl] undecanoate739270: Inhibition of mitochondrial ETC complex 1 in human T47D cells assessed as inhibition of 1% O2-induced HIF1 activation incubated for 30 mins prior to 1% O2-challenge measured after 16 hrs by luciferase reporter assayic500.8700uM
[(E,3R)-2-hydroxy-2,6-dimethyl-8-(2-oxochromen-7-yl)oxyoct-6-en-3-yl] (9Z,12Z)-octadeca-9,12-dienoate739270: Inhibition of mitochondrial ETC complex 1 in human T47D cells assessed as inhibition of 1% O2-induced HIF1 activation incubated for 30 mins prior to 1% O2-challenge measured after 16 hrs by luciferase reporter assayic500.9200uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148853: Binding affinity to human NDUFS2 incubated for 45 mins by Kinobead based pull down assaykd1.2362uM
[(E,3R)-2-hydroxy-2,6-dimethyl-8-(2-oxochromen-7-yl)oxyoct-6-en-3-yl] octanoate739270: Inhibition of mitochondrial ETC complex 1 in human T47D cells assessed as inhibition of 1% O2-induced HIF1 activation incubated for 30 mins prior to 1% O2-challenge measured after 16 hrs by luciferase reporter assayic503.0800uM
[(2S,3R,4R)-2-(4-hydroxy-3-methoxyphenyl)-4-[(4-hydroxy-3-methoxyphenyl)methyl]oxolan-3-yl]methyl 3-methylbutanoate739269: Inhibition of mitochondrial ETC complex 1 in human T47D cells assessed as inhibition of 1,10-phenanthroline-induced HIF1 activation incubated for 30 mins prior to 1,10-phenanthroline-challenge measured after 16 hrs by luciferase reporter assayic504.9000uM

CTD chemical–gene interactions

46 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Acetaminophenaffects cotreatment, decreases expression3
bisphenol Aincreases expression2
sodium arsenitedecreases expression, affects cotreatment, increases abundance2
Arsenicincreases methylation, affects cotreatment, decreases expression, increases abundance2
Valproic Acidincreases expression, increases methylation2
Particulate Matterdecreases expression, increases abundance, increases expression2
triphenyl phosphateaffects expression1
sodium arsenatedecreases expression1
beta-lapachoneincreases expression1
perfluorooctanoic aciddecreases expression1
manganese chloridedecreases expression, increases abundance, affects cotreatment1
di-n-butylphosphoric acidaffects expression1
2,3,5-(triglutathion-S-yl)hydroquinoneincreases ADP-ribosylation1
CGP 52608affects binding, increases reaction1
jinfukangincreases expression1
(+)-JQ1 compounddecreases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Arsenic Trioxideincreases expression1
Aerosolsdecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Atrazinedecreases expression1
Benzo(a)pyreneincreases methylation1
Cocaineaffects expression1
Doxorubicinincreases expression1
Isoniaziddecreases expression1
Ivermectindecreases expression1
Leaddecreases expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1

ChEMBL screening assays

11 unique, capped per target: 10 binding, 1 functional

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL2353025BindingInhibition of mitochondrial ETC complex 1 in human T47D cells assessed as inhibition of 1% O2-induced HIF1 activation at 30 uM incubated for 30 mins prior to 1% O2-challenge measured after 16 hrs by luciferase reporter assaySemisynthetic studies identify mitochondria poisons from botanical dietary supplements–geranyloxycoumarins from Aegle marmelos. — Bioorg Med Chem
CHEMBL5210044FunctionalAffinity Phenotypic Cellular interaction (Proliferation assay (CellTiter-Glo ATP assay in human lung H1299 cells)) EUB0000752a NDUFS2Affinity Phenotypic Cellular Literature for EUbOPEN Chemogenomics Library wave 3

Cellosaurus cell lines

8 cell lines: 5 cancer cell line, 2 transformed cell line, 1 finite cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_C0D2HEK293 NDUSF2 KOTransformed cell lineFemale
CVCL_D1P5Abcam K-562 NDUFS2 KOCancer cell lineFemale
CVCL_D2KQAbcam Raji NDUFS2 KOCancer cell lineMale
CVCL_D9L4Ubigene HEK293 NDUFS2 KOTransformed cell lineFemale
CVCL_EQ488807Finite cell lineFemale
CVCL_TA18HAP1 NDUFS2 (-) 1Cancer cell lineMale
CVCL_TA19HAP1 NDUFS2 (-) 2Cancer cell lineMale
CVCL_WQ07Abcam Jurkat NDUFS2 KOCancer cell lineMale

Clinical trials (associated diseases)

31 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT03293524PHASE3COMPLETEDEfficacy & Safety Study of Bilateral IVT Injection of GS010 in LHON Subjects Due to the ND4 Mutation for up to 1 Year
NCT03406104PHASE3COMPLETEDRESCUE and REVERSE Long-term Follow-up
NCT07406854PHASE3ACTIVE_NOT_RECRUITINGA Phase 3, Multicenter, Randomized, Double-Masked, Sham-Controlled Clinical Trial for Leber’s Hereditary Optic Neuropathy (LHON) Associated With ND4 Mutation
NCT05162768PHASE3COMPLETEDStudy to Evaluate Efficacy and Safety of Elamipretide in Subjects With Primary Mitochondrial Disease From Nuclear DNA Mutations (nPMD)
NCT02176733PHASE2UNKNOWNTrial of Cyclosporine in the Acute Phase of Leber Hereditary Optic Neuropathy
NCT02544217PHASE1COMPLETEDA Dose-escalating Clinical Trial With KH176
NCT07258667PHASE1NOT_YET_RECRUITINGPilot Study of the Efficacy of Nicotinamide (Vitamin B3) in Leber’s Hereditary Optic Neuropathy
NCT01064505PHASE1COMPLETEDSafety Study of a Single IVT Injection of QPI-1007 in Chronic Optic Nerve Atrophy and Recent Onset NAION Patients
NCT05147701PHASE1RECRUITINGSafety of Cultured Allogeneic Adult Umbilical Cord Derived Mesenchymal Stem Cells for NAION
NCT03153293PHASE2/PHASE3UNKNOWNA Single Intravitreal Injection of rAAV2-ND4 for the Treatment of Leber’s Hereditary Optic Neuropathy
NCT02064569PHASE1/PHASE2COMPLETEDSafety Evaluation of Gene Therapy in Leber Hereditary Optic Neuropathy (LHON) Patients
NCT05293626PHASE1/PHASE2ACTIVE_NOT_RECRUITINGGene Therapy Clinical Trial for the Treatment of Leber’s Hereditary Optic Neuropathy Associated With ND4 Mutations
NCT05820152PHASE1/PHASE2TERMINATEDGene Therapy Clinical Trial for the Treatment of Leber’s Hereditary Optic Neuropathy Associated With ND1 Mutations
NCT01267422Not specifiedCOMPLETEDSafety and Efficacy Study of rAAV2-ND4 Treatment of Leber Hereditary Optic Neuropathy (LHON)
NCT01803906Not specifiedENROLLING_BY_INVITATIONTissue Sample Study for Mitochondrial Disorders
NCT01892943Not specifiedCOMPLETEDLeber Hereditary Optic Neuropathy (LHON) Historical Case Record Survey
NCT03011541Not specifiedRECRUITINGStem Cell Ophthalmology Treatment Study II
NCT03295071Not specifiedCOMPLETEDREALITY LHON Registry
NCT03428178Not specifiedUNKNOWNEfficacy Study of Gene Therapy for The Treatment of Acute LHON Onset Within Three Months
NCT03475173Not specifiedRECRUITINGNew Non-invasive Modalities for Assessing Retinal Structure and Function
NCT03672968Not specifiedNO_LONGER_AVAILABLEEAP_GS010_single Patient
NCT05554835Not specifiedRECRUITINGGlobal Registry and Natural History Study for Mitochondrial Disorders
NCT06376279Not specifiedENROLLING_BY_INVITATIONGenetic Diagnosis in Inborn Errors of Metabolism
NCT06682819Not specifiedRECRUITINGMetabolomics Analysis According to the Retinal Nerve Fiber Layer in Patients With NOHL Mutations (MétabOCT)
NCT02882477PHASE2/PHASE3UNKNOWNTreatment of Wolfram Syndrome Type 2 With the Chelator Deferiprone and Incretin Based Therapy
NCT01834079PHASE1/PHASE2UNKNOWNStudy the Safety and Efficacy of Bone Marrow Derived Autologous Cells for the Treatment of Optic Nerve Disease
NCT04680143PHASE1/PHASE2COMPLETEDSystemic Erythropoietin Injection in Patients Having Optic Atrophy
NCT04580979Not specifiedCOMPLETEDNatural History Study of FDXR Mutation-related Mitochondriopathy
NCT04594590Not specifiedCOMPLETEDNatural History Study of SLC25A46 Mutation-related Mitochondriopathy
NCT04723160Not specifiedCOMPLETEDComputer Aided Diagnosis of Multiple Eye Fundus Diseases From Color Fundus Photograph
NCT06390579Not specifiedCOMPLETEDBuilding Research With Artificial Intelligence in Neuro-Ophthalmology