NDUFV2
protein-codingNADH:ubiquinone oxidoreductase core subunit V2, the group of NADH:ubiquinone oxidoreductase core subunits
Gene summary
The NADH-ubiquinone oxidoreductase complex (complex I) of the mitochondrial respiratory chain catalyzes the transfer of electrons from NADH to ubiquinone, and consists of at least 43 subunits. The complex is located in the inner mitochondrial membrane. This gene encodes the 24 kDa subunit of complex I, and is involved in electron transfer. Mutations in this gene are implicated in Parkinson's disease, bipolar disorder, schizophrenia, and have been found in one case of early onset hypertrophic cardiomyopathy and encephalopathy. A non-transcribed pseudogene of this locus is found on chromosome 19. [provided by RefSeq, Oct 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~31.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0032612
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *NDUFV2* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of December 4, 2023. The *NDUFV2* gene encodes the NADH:ubiquinone oxidoreductase (complex I) flavoprotein 2, a core subunit of mitochondrial complex I. Defects of this protein lead to complex I deficiency. *NDUFV2* was first reported in relation to autosomal recessive primary mitochondrial disease in 2003 (PMID: 12754703), in a proband with hypertrophic cardiomyopathy, encephalopathy, feeding difficulty, and growth failure who died at three months of age. While various names could be given to the constellation of features seen in those with *NDUFV2*-related disease, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the *NDUFV2* phenotype has been lumped into one disease entity according to the ClinGen Lumping and Splitting Framework. Of note, *NDUFV2* was previously curated by this GCEP on November 20, 2019 (SOP Version 7) as having a Limited association with Leigh Syndrome Spectrum (LSS). The scope of this current curation encompassed cases of primary mitochondrial disease, which includes LSS. Evidence supporting the gene-disease relationship between *NDUFV2* and primary mitochondrial disease includes case-level data and experimental data. This curation includes nine unique variants in ten probands from nine publications (PMIDs: 12754703, 19167255, 26008862, 33811136, 34405929, 28429146, 30369941, 34276053, 30831263). Variant types included five missense, one frameshift, one stop-gain, one intragenic deletion and one recurrent splice region variant (NM_021074.5:c.120+5_120+8del). Affected individuals present with a broad phenotypic spectrum of generally severe disease which includes LSS. Clinical features include developmental regression, seizures, progressive spasticity, microcephaly, hypotonia, hypertrophic cardiomyopathy, optic atrophy, feeding difficulty, and failure to thrive. The age of onset ranges from birth to early infancy. Loss of function is implicated as the mechanism of disease. This gene-disease association is also supported by known biochemical function and a C. elegans model system (PMIDs: 33340416. 19672299). In summary, there is Definitive evidence to support this gene-disease relationship, including that more than three years have elapsed from the first proposal of the association. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on December 4, 2023 (SOP Version 9).
Inheritance Pattern: AR
Disease ID:MONDO:0009723
Submitter: ClinGen
The relationship between NDUFV2 and Leigh syndrome spectrum was evaluated using the ClinGen Clinical Validity Framework as of November 20, 2019. The NDUFV2 gene encodes the NADH:ubiquinone oxidoreductase (complex I) flavoprotein 2, a core subunit of mitochondrial complex I. Defects of this protein lead to complex I deficiency. The NDUFV2 gene has been reported in relation to autosomal recessive Leigh syndrome spectrum in a single publication in 2011 (PMID: 26008862). Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included one homozygous variant identified in one case in one publication (PMID: 26008862). 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 interactions (PMID: 27509854). In addition, variants in NDUFV2 have been associated with other phenotypes outside the scope of the Leigh syndrome spectrum gene-disease curation. In summary, there is limited evidence to support a 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 November 20, 2019 (SOP Version 7).
Inheritance Pattern: AR
Disease ID:MONDO:0032612
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0032612
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0032612
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0100133
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Cardiovascular; Gastrointestinal; 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
Comments: Medical treatment (eg, riboflavin, ubiquinol) may be beneficial; Individuals may have cardiac involvement
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NDUFV2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021074.5. 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 | 14 | 16 | |||
| missense | 3 | 63 | 3 | 69 | ||
| nonsense | 2 | 2 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 8 | 4 | 12 | |||
| splice donor/acceptor (+/-2bp) | 1 | 1 | 6 | 8 | ||
| Total | 9 | 9 | 73 | 17 | 0 | 108 |
Highest pathogenic variant AF is 0.00013833659
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_066552.2 | 8 | MANE Select | |
| Ensembl | ENSP00000327268.6 | 8 | MANE Select | |
| Ensembl | ENSP00000382908.1 | 9 | Standard | |
| Ensembl | ENSP00000382908.1 | 9 | 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
- nervous system development
- mitochondrial respiratory chain complex I assembly
- cardiac muscle tissue development
Molecular Function
- NADH dehydrogenase activity
- protein binding
- NADH dehydrogenase (ubiquinone) activity
- electron transfer activity
- metal ion binding
Cellular Component
- mitochondrion
- mitochondrial inner membrane
- mitochondrial respiratory chain complex I
- myelin sheath
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000318388
- Coding exons
- 8
- Length
- 31716
- Individuals with no LoFs
- 125685
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 63
- Defined
- 125748
- p
- 0.000251
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.555 | 149 | 131 | 1.14 | 0.00000603 | 1608 |
| Missense (PolyPhen) | 51 | 47.298 | 1.0783 | 578 | ||
| Synonymous | 0.0650 | 42 | 42.5 | 0.987 | 0.00000194 | 477 |
| Loss of Function | 2.02 | 6 | 14.2 | 0.422 | 7.30e-7 | 172 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0.00042 | 0.00042 | rare |
| European (Non-Finnish) | 0.00030 | 0.00030 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for 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 (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.216
Intolerance Scores
- LoFtool
- 0.814
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.553
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |