NDUFC2
protein-codingNADH:ubiquinone oxidoreductase subunit C2, the group of NADH:ubiquinone oxidoreductase supernumerary subunits
Gene summary
Predicted to enable NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial respiratory chain complex I assembly. Located in mitochondrial inner membrane. Part of respiratory chain complex I. Implicated in nuclear type mitochondrial complex I deficiency and stroke. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *NDUFC2* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of December 18, 2023. The *NDUFC2* gene encodes the NADH:ubiquinone oxidoreductase (complex I) subunit C2, which also plays a role in complex I assembly. Defects of this protein lead to complex I deficiency. The first and only report of *NDUFC2* in relation to autosomal recessive primary mitochondrial disease was in 2020 (PMID:32969598) in two unrelated probands with Leigh syndrome spectrum (LSS). While various names could be given to the constellation of features seen in those with *NDUFC2*-related disease, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the *NDUFC2* phenotype has been lumped into one disease entity according to the ClinGen Lumping and Splitting Framework. Of note, *NDUFC2* was first curated by this GCEP for its association with LSS on November 23, 2020 (SOP Version 7), with a final classification of Moderate. This current curation for the association with primary mitochondrial disease includes cases with LSS. Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included two variants (homozygous missense and homozygous stop-loss) identified in two cases in one publication (PMID: 32969598). This gene-disease association is also supported by functional implication its known biochemical function (PMID: 27509854) and by complexome profiling in patient cells (PMID: 32969598). In summary, there is moderate evidence to support the relationship between *NDUFC2* and primary mitochondrial disease. While more evidence is needed to establish this relationship definitively, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on December 18, 2023 (SOP Version 9).
Inheritance Pattern: Unknown
Disease ID:MONDO:0030902
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0030902
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009723
Submitter: ClinGen
The relationship between NDUFC2 and Leigh syndrome spectrum was evaluated using the ClinGen Clinical Validity Framework as of November 23, 2020. The NDUFC2 gene encodes the NADH:ubiquinone oxidoreductase (complex I) subunit C2, which also plays a role in complex I assembly. Defects of this protein lead to complex I deficiency. The NDUFC2 gene was first reported in relation to autosomal recessive Leigh syndrome spectrum in 2020 (PMID: 32969598). Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included two variants identified in two cases in one publication (PMID: 32969598). No segregation data were available. Loss of function is implicated as the mechanism of disease. This gene-disease association is also supported by known protein interaction, functional alteration in non-patient cells, and functional alteration in patient cells (PMIDs: 27509854, 27626371, 32969598). In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the NICHD U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on November 23, 2020 (SOP Version 7).
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Cardiovascular; Neurologic; Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NDUFC2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004549.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 1 | 2 | 3 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 1 | 2 | 2 | 0 | 6 |
Highest pathogenic variant AF is 0.000056998473
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004540.1 | 3 | MANE Select | |
| Ensembl | ENSP00000281031.4 | 3 | MANE Select | |
| RefSeq | NP_001190983.1 | 3 | Standard | |
| RefSeq | NP_001190984.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Retrograde endocannabinoid signaling - Homo sapiens (human)
- Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human)
- Alzheimer,s disease - Homo sapiens (human)
- Huntington,s disease - Homo sapiens (human)
- Thermogenesis - Homo sapiens (human)
Biological Process
- mitochondrial electron transport, NADH to ubiquinone
- mitochondrial respiratory chain complex I assembly
- neutrophil degranulation
Molecular Function
- NADH dehydrogenase (ubiquinone) activity
Cellular Component
- cytoplasm
- mitochondrion
- mitochondrial inner membrane
- mitochondrial respiratory chain complex I
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000281031
- Coding exons
- 3
- Length
- 11916
- Individuals with no LoFs
- 117701
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 117703
- p
- 0.00000850
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.238 | 62 | 67.5 | 0.919 | 0.00000388 | 748 |
| Missense (PolyPhen) | 32 | 34.445 | 0.92901 | 340 | ||
| Synonymous | 0.0640 | 25 | 25.4 | 0.984 | 0.00000124 | 232 |
| Loss of Function | 1.79 | 0 | 3.73 | 0.00 | 1.54e-7 | 57 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- 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. {ECO:0000269|PubMed:27626371}.;
Recessive Scores
- pRec
- 0.0703
Intolerance Scores
- LoFtool
- 0.493
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 62.74
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- H
- Indispensability pred.
- N
- Indispensability score
- 0.0733
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |