Combined oxidative phosphorylation deficiency

disease
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Summary

Combined oxidative phosphorylation deficiency (MONDO:0000732) is a disease (an umbrella term covering 58 Mondo subtypes) with 6 cohort genes.

At a glance

  • Umbrella term: 58 Mondo subtypes
  • Cohort genes: 6
  • ClinVar variants: 396

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namecombined oxidative phosphorylation deficiency
Mondo IDMONDO:0000732
OMIM609060
DOIDDOID:0060286
ICD-111953023896
UMLSC4540031
MedGen1626645
GARD0012893
Is cancer (heuristic)no

Data availability: 396 ClinVar variants · 2 GenCC gene-disease records.

Disease family

An umbrella term covering 58 Mondo subtypes.

Classification path: disease › human disease › disease by developmental or physiological process › metabolic diseasedevelopmental anomaly of metabolic origininborn mitochondrial metabolism disordermitochondrial oxidative phosphorylation disordercombined oxidative phosphorylation deficiency

Related subtypes (47): mitochondrial respiratory chain complex deficiency, myopathy, lactic acidosis, and sideroblastic anemia, optic atrophy 3, autosomal dominant optic atrophy, classic form, Leigh syndrome, mitochondrial non-syndromic sensorineural hearing loss, maternally-inherited diabetes and deafness, chronic diarrhea with villous atrophy, Kearns-Sayre syndrome, Leber hereditary optic neuropathy, NARP syndrome, deafness, aminoglycoside-induced, hereditary spastic paraplegia 7, spinocerebellar ataxia type 28, leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome, spastic ataxia 3, pontocerebellar hypoplasia type 6, autosomal recessive optic atrophy, OPA7 type, acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins, congenital cataract-progressive muscular hypotonia-hearing loss-developmental delay syndrome, spastic ataxia 4, hyperuricemia-pulmonary hypertension-renal failure-alkalosis syndrome, hereditary spastic paraplegia 55, cataract-growth hormone deficiency-sensory neuropathy-sensorineural hearing loss-skeletal dysplasia syndrome, Charcot-Marie-Tooth disease recessive intermediate D, autosomal dominant mitochondrial myopathy with exercise intolerance, Charcot-Marie-Tooth disease type 4K, hydrops-lactic acidosis-sideroblastic anemia-multisystemic failure syndrome, hereditary spastic paraplegia 77, fatal infantile encephalocardiomyopathy, FASTKD2-related infantile mitochondrial encephalomyopathy, autosomal dominant optic atrophy and peripheral neuropathy, ataxia neuropathy spectrum, maternally-inherited mitochondrial dystonia, Perrault syndrome, hypertrophic cardiomyopathy and renal tubular disease due to mitochondrial DNA mutation, adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy, mitochondrial DNA maintenance syndrome, coenzyme Q10 deficiency, mitochondrial DNA depletion syndrome, periodic paralysis with later-onset distal motor neuropathy, non-progressive predominantly posterior cavitating leukoencephalopathy with peripheral neuropathy, Zellweger-like syndrome without peroxisomal anomalies, maternally-inherited progressive external ophthalmoplegia, Leber plus disease, encephalopathy due to mitochondrial and peroxisomal fission defect, severe neonatal lactic acidosis due to NFS1-ISD11 complex deficiency

Subtypes (58): severe X-linked mitochondrial encephalomyopathy, hepatoencephalopathy due to combined oxidative phosphorylation defect type 1, combined oxidative phosphorylation defect type 2, fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3, combined oxidative phosphorylation defect type 4, hypotonia with lactic acidemia and hyperammonemia, combined oxidative phosphorylation defect type 7, combined oxidative phosphorylation defect type 8, combined oxidative phosphorylation defect type 9, mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency, combined oxidative phosphorylation defect type 11, leukoencephalopathy-thalamus and brainstem anomalies-high lactate syndrome, combined oxidative phosphorylation defect type 13, combined oxidative phosphorylation defect type 14, combined oxidative phosphorylation defect type 15, infantile hypertrophic cardiomyopathy due to MRPL44 deficiency, combined oxidative phosphorylation defect type 17, growth and developmental delay-hypotonia-vision impairment-lactic acidosis syndrome, combined oxidative phosphorylation deficiency 19, combined oxidative phosphorylation defect type 20, combined oxidative phosphorylation defect type 21, mitochondrial proton-transporting ATP synthase complex deficiency, combined oxidative phosphorylation defect type 23, combined oxidative phosphorylation defect type 24, combined oxidative phosphorylation defect type 25, combined oxidative phosphorylation defect type 26, combined oxidative phosphorylation defect type 27, combined oxidative phosphorylation deficiency 28, combined oxidative phosphorylation deficiency 29, combined oxidative phosphorylation defect type 30, lethal left ventricular non-compaction-seizures-hypotonia-cataract-developmental delay syndrome, combined oxidative phosphorylation deficiency 40, combined oxidative phosphorylation deficiency 41, combined oxidative phosphorylation deficiency 42, combined oxidative phosphorylation deficiency 43, combined oxidative phosphorylation deficiency 44, combined oxidative phosphorylation deficiency 52, combined oxidative phosphorylation deficiency 53, combined oxidative phosphorylation deficiency 54, combined oxidative phosphorylation deficiency 37, combined oxidative phosphorylation deficiency 38, combined oxidative phosphorylation deficiency 39, combined oxidative phosphorylation deficiency 45, combined oxidative phosphorylation deficiency 46, combined oxidative phosphorylation deficiency 47, combined oxidative phosphorylation deficiency 48, combined oxidative phosphorylation deficiency 51, combined oxidative phosphorylation deficiency 32, combined oxidative phosphorylation deficiency 33, combined oxidative phosphorylation deficiency 34, combined oxidative phosphorylation deficiency 35, combined oxidative phosphorylation deficiency 36, combined oxidative phosphorylation deficiency 55, combined oxidative phosphorylation deficiency 56, combined oxidative phosphorylation deficiency 57, combined oxidative phosphorylation deficiency 58, combined oxidative phosphorylation deficiency 59, combined oxidative phosphorylation deficiency 60

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

396 retrieved; paginated sample, class counts are floors:

178 likely benign, 154 uncertain significance, 24 conflicting classifications of pathogenicity, 19 benign/likely benign, 14 benign, 5 pathogenic/likely pathogenic, 2 likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
162479NM_004208.4(AIFM1):c.1264C>T (p.Arg422Trp)AIFM1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
374094NM_004208.4(AIFM1):c.1019T>C (p.Met340Thr)AIFM1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
30598NM_024996.7(GFM1):c.748C>T (p.Arg250Trp)GFM1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
509754NM_024996.7(GFM1):c.689+908G>AGFM1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
162480NM_004208.4(AIFM1):c.1265G>A (p.Arg422Gln)RAB33APathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2933356NM_004208.4(AIFM1):c.1195G>A (p.Gly399Ser)AIFM1Likely pathogeniccriteria provided, single submitter
162481NM_004208.4(AIFM1):c.1424C>T (p.Pro475Leu)RAB33ALikely pathogeniccriteria provided, single submitter
1204071NM_004208.4(AIFM1):c.8G>A (p.Arg3Gln)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1357142NM_004208.4(AIFM1):c.1663G>A (p.Val555Ile)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
162477NM_004208.4(AIFM1):c.1030C>T (p.Leu344Phe)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1954172NM_004208.4(AIFM1):c.174T>A (p.Gly58=)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2136048NM_004208.4(AIFM1):c.1020G>T (p.Met340Ile)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
214081NM_004208.4(AIFM1):c.1642C>T (p.Pro548Ser)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2426260NC_000023.10:g.(?128674417)(129299630_?)delAIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
243069NM_004208.4(AIFM1):c.1388G>T (p.Arg463Ile)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2934504NM_004208.4(AIFM1):c.258G>T (p.Lys86Asn)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
373913NM_004208.4(AIFM1):c.1646C>T (p.Ala549Val)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
411665NM_004208.4(AIFM1):c.1643C>T (p.Pro548Leu)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
518002NM_004208.4(AIFM1):c.1036G>A (p.Glu346Lys)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
547098NM_004208.4(AIFM1):c.556A>G (p.Asn186Asp)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
594797NM_004208.4(AIFM1):c.952G>A (p.Ala318Thr)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
640384NM_004208.4(AIFM1):c.1075+4G>CAIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
655000NM_004208.4(AIFM1):c.893G>A (p.Arg298Gln)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
660192NM_004208.4(AIFM1):c.141A>C (p.Glu47Asp)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
836326NM_004208.4(AIFM1):c.724A>G (p.Met242Val)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
857026NM_004208.4(AIFM1):c.340G>A (p.Ala114Thr)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
958283NM_004208.4(AIFM1):c.1045A>G (p.Ser349Gly)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
982823NM_004208.4(AIFM1):c.506C>T (p.Pro169Leu)AIFM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
445310NM_004208.4(AIFM1):c.170C>G (p.Ser57Cys)RAB33AConflicting classifications of pathogenicitycriteria provided, conflicting classifications
641733NM_004208.4(AIFM1):c.1006G>A (p.Glu336Lys)RAB33AConflicting classifications of pathogenicitycriteria provided, conflicting classifications

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 5 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
OXA1LModerateAutosomal recessivecombined oxidative phosphorylation deficiency
TOMM70LimitedAutosomal recessivecombined oxidative phosphorylation deficiency4

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
GFM1Orphanet:137681Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1
AIFM1Orphanet:101078X-linked Charcot-Marie-Tooth disease type 4
AIFM1Orphanet:139583X-linked hereditary sensory and autonomic neuropathy with deafness
AIFM1Orphanet:238329Severe X-linked mitochondrial encephalomyopathy
AIFM1Orphanet:83629Leukoencephalopathy-spondyloepimetaphyseal dysplasia syndrome

Cohort genes → proteins

6 cohort genes, 6 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence6

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
TOMM70HGNC:11985ENSG00000154174O94826Mitochondrial import receptor subunit TOM70gencc
OXA1LHGNC:8526ENSG00000155463Q15070Mitochondrial inner membrane protein OXA1Lgencc
GFM1HGNC:13780ENSG00000168827Q96RP9Elongation factor G, mitochondrialclinvar
TAMM41HGNC:25187ENSG00000144559Q96BW9Phosphatidate cytidylyltransferase, mitochondrialclinvar
AIFM1HGNC:8768ENSG00000156709O95831Apoptosis-inducing factor 1, mitochondrialclinvar
RAB33AHGNC:9773ENSG00000134594Q14088Ras-related protein Rab-33Aclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
TOMM70Mitochondrial import receptor subunit TOM70Acts as a receptor of the preprotein translocase complex of the outer mitochondrial membrane (TOM complex).
OXA1LMitochondrial inner membrane protein OXA1LMitochondrial membrane insertase that mediates the cotranslational insertion of integral membrane proteins into the mitochondrial inner membrane.
GFM1Elongation factor G, mitochondrialMitochondrial GTPase that catalyzes the GTP-dependent ribosomal translocation step during translation elongation.
TAMM41Phosphatidate cytidylyltransferase, mitochondrialCatalyzes the conversion of phosphatidic acid (PA) to CDP-diacylglycerol (CDP-DAG), an essential intermediate in the synthesis of phosphatidylglycerol, cardiolipin and phosphatidylinositol.
AIFM1Apoptosis-inducing factor 1, mitochondrialFunctions both as NADH oxidoreductase and as regulator of apoptosis.
RAB33ARas-related protein Rab-33AThe small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 5 · Druggable fraction: 0.17

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Other/Unknown51.5×0.348
Enzyme (other)12.0×0.407

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
TOMM70Other/UnknownnoTPR-like_helical_dom_sf, TPR_rpt
OXA1LOther/UnknownnoYidC/ALB3/OXA1/COX18, YidC/Oxa/ALB_C
GFM1Other/UnknownnoEFG_V-like, T_Tr_GTP-bd_dom, EFTu-like_2
TAMM41Other/UnknownnoTam41
AIFM1Enzyme (other)yes7.1.1.2FAD/NAD-linked_Rdtase_dimer_sf, FAD/NAD-binding_dom, AIF_C
RAB33AOther/UnknownnoSmall_GTPase, Small_GTP-bd, P-loop_NTPase

Expression context

Cohort genes with no expression data: 0.

4 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)6
unknown0

Top tissues across cohort

TissueCohort genes
endothelial cell2
Brodmann (1909) area 231
gluteal muscle1
body of pancreas1
diaphragm1
hindlimb stylopod muscle1
adrenal tissue1
biceps brachii1
granulocyte1
male germ line stem cell (sensu Vertebrata) in testis1
primordial germ cell in gonad1
adult mammalian kidney1
apex of heart1
heart left ventricle1
C1 segment of cervical spinal cord1
cortical plate1
prefrontal cortex1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
TOMM70299ubiquitousmarkerendothelial cell, gluteal muscle, Brodmann (1909) area 23
OXA1L290ubiquitousmarkerhindlimb stylopod muscle, body of pancreas, diaphragm
GFM1271ubiquitousmarkerendothelial cell, biceps brachii, adrenal tissue
TAMM41136ubiquitousyesprimordial germ cell in gonad, granulocyte, male germ line stem cell (sensu Vertebrata) in testis
AIFM1273ubiquitousmarkerapex of heart, adult mammalian kidney, heart left ventricle
RAB33A207ubiquitousyescortical plate, C1 segment of cervical spinal cord, prefrontal cortex

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
GFM15,789
AIFM14,780
OXA1L2,947
TOMM702,629
RAB33A1,603
TAMM41869

Intra-cohort edges

ABSources
OXA1LTOMM70string_interaction

Structural data

PDB: 4 · AlphaFold-only: 2 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
AIFM1O9583126
OXA1LQ1507017
GFM1Q96RP95
TOMM70O948263

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
RAB33AQ1408881.85
TAMM41Q96BW973.42

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 13. Enrichment computed across 6 evidence-associated genes (4 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Mitochondrial translation elongation263.4×0.005GFM1, OXA1L
PINK1-PRKN Mediated Mitophagy189.2×0.039TOMM70
SARS-CoV-1 activates/modulates innate immune responses168.0×0.039TOMM70
TBC/RABGAPs164.9×0.039RAB33A
DDX58/IFIH1-mediated induction of interferon-alpha/beta163.4×0.039TOMM70
RAB geranylgeranylation143.3×0.039RAB33A
Mitochondrial protein import142.0×0.039TOMM70
Complex I biogenesis141.4×0.039OXA1L
Mitochondrial translation initiation131.7×0.042OXA1L
Mitochondrial ribosome-associated quality control130.7×0.042OXA1L
Mitochondrial translation termination127.4×0.042OXA1L
SARS-CoV-2 activates/modulates innate and adaptive immune responses122.3×0.048TOMM70
Ub-specific processing proteases113.3×0.073TOMM70

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
protein import into mitochondrial intermembrane space1936.2×0.009AIFM1
response to thyroxine1936.2×0.009TOMM70
protein import into the intermembrane space via the disulfide relay system1936.2×0.009AIFM1
mitochondrial translational elongation1702.2×0.009GFM1
mitochondrial protein quality control1702.2×0.009OXA1L
cardiolipin biosynthetic process1561.7×0.009TAMM41
protein insertion into mitochondrial inner membrane from matrix1561.7×0.009OXA1L
mitochondrial respiratory chain complex assembly1468.1×0.009AIFM1
negative regulation of oxidoreductase activity1468.1×0.009OXA1L
positive regulation of necroptotic process1468.1×0.009AIFM1
cellular response to aldosterone1401.2×0.010AIFM1
mitochondrial proton-transporting ATP synthase complex assembly1351.1×0.010OXA1L
negative regulation of ATP-dependent activity1280.9×0.011OXA1L
response to L-glutamate1280.9×0.011AIFM1
negative regulation of cell growth involved in cardiac muscle cell development1234.1×0.011TOMM70
CDP-diacylglycerol biosynthetic process1216.1×0.011TAMM41
protein insertion into mitochondrial inner membrane1216.1×0.011TOMM70
protein insertion into mitochondrial outer membrane1216.1×0.011TOMM70
Rab protein signal transduction1165.2×0.014RAB33A
cellular response to nitric oxide1156.0×0.014AIFM1
antigen processing and presentation1117.0×0.017RAB33A
protein import into mitochondrial matrix1117.0×0.017TOMM70
protein tetramerization1104.0×0.018OXA1L
obsolete protein targeting to mitochondrion196.8×0.019TOMM70
positive regulation of defense response to virus by host187.8×0.019TOMM70
obsolete positive regulation of protein targeting to mitochondrion182.6×0.019TOMM70
activation of innate immune response180.2×0.019TOMM70
intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress180.2×0.019AIFM1
mitochondrial respiratory chain complex I assembly168.5×0.021OXA1L
cellular response to estradiol stimulus168.5×0.021AIFM1

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 6

Druggability breadth: 4 of 6 evidence-associated genes (67%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
TOMM7000
OXA1L00
GFM100
TAMM4100
AIFM100
RAB33A00

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
TOMM702Binding:2
AIFM12Binding:2
OXA1L1Binding:1
GFM11Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
AIFM17.1.1.2NADH:ubiquinone reductase (H+-translocating)

Pharmacogenomics

Cohort genes with a PharmGKB record: 6; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1AIFM1
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug5TOMM70, OXA1L, GFM1, TAMM41, RAB33A

Undrugged target profiles

6 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
TOMM702
OXA1L1
GFM11
TAMM410
AIFM12
RAB33A0

Clinical trials & evidence

Clinical trials

Clinical trials: 0.