NDUFV2

protein-coding

NADH: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

NM_021074.5

Inheritance

AR

ClinVar variants

P:18U:73B:17

Top phenotype

Mitochondrial complex I deficiency, nuclear type 7

gnomAD constraint

pLI —, LoF o/e 0.42

Max pathogenic AF

—

Genomic locus

chr18:9,102,630-9,134,345

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~31.7 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

mitochondrial complex I deficiency, nuclear type 7MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0032612

Submitter: G2P

mitochondrial diseaseDEFINITIVE

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).

Leigh syndromeLIMITED

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).

mitochondrial complex I deficiency, nuclear type 7STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032612

Submitter: PanelApp Australia

mitochondrial complex I deficiency, nuclear type 7MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0032612

Submitter: Ambry Genetics

mitochondrial complex I deficiency, nuclear type 7STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032612

Submitter: Labcorp Genetics (formerly Invitae)

mitochondrial complex I deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0100133

Submitter: Orphanet

Clinical Genomic Database (CGD)

Mitochondrial complex I deficiency, nuclear type 7AR

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

Refs: 11743516; 12754703; 21548921Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NDUFV2 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 93
Inborn genetic diseasesTotal: 33
Mitochondrial complex I deficiency, nuclear type 7Total: 20
Mitochondrial complex I deficiency, nuclear type 1Total: 11
not specifiedTotal: 9
NDUFV2-related disorderTotal: 5

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
14
clinvar
16
missense
3
clinvar
63
clinvar
3
clinvar
69
nonsense
2
clinvar
2
start loss
1
clinvar
1
frameshift
8
clinvar
4
clinvar
12
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
6
clinvar
8
Total9973170108

Highest pathogenic variant AF is 0.00013833659

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 74 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_021074.5RefSeqNP_066552.28MANE Select
ENST00000318388.11EnsemblENSP00000327268.68MANE Select
ENST00000400033.1EnsemblENSP00000382908.19Standard
ENST00000400033.2EnsemblENSP00000382908.19Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.5551491311.140.000006031608
Missense (PolyPhen)5147.2981.0783578
Synonymous0.06504242.50.9870.00000194477
Loss of Function2.02614.20.4227.30e-7172

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish00.0absent
East Asian0.000380.00038rare
Finnish0.000420.00042rare
European (Non-Finnish)0.000300.00030rare
South Asian0.000230.00023rare
Other0.000490.00049rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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