Background
Methods
Clinical and biochemical investigation of patients
Patient N° | Age-range at investigations (years) | Sex | Muscle histology | Biochemical defect | mtDNA deletions | Clinical presentation |
---|---|---|---|---|---|---|
1 | < 1 | M | N | ↓CIII, IV | No | Encephalopathy with spastic dystonia |
2 | < 1 | F | N | N | No | Leigh syndrome, growth retardation, dystonia |
3 | < 1 | F | N | ↓CI | No | Encephalopathy, hepatomegaly, epilepsy, leukodystrophy |
4 | < 1 | M | lipidosis | N(m) + impaired assembly CI, N(l) | No | Leigh syndrome |
5 | < 1 | F | N | ↓CI | No | Spastic tetraparesia, growth retardation |
6 | < 1 | F | NA | NA | NA | Congenital cataract, microphtalmia, hypotonia, myocardic dysfunction |
7 | < 1 | M | N | Multi | No | Leigh syndrome, growth retardation, myoclonic epilepsy, chronic diarrhea, vascular purpura, lactic acidosis, death at 3 years-old |
8 | < 1 | M | RRF lipidosis | N | No | Neonatal hypotonia, growth retardation, myopathy, cardiopulmonary failure, methylglutaconic aciduria |
9 | < 1 | M | NA | ↓CII, III, IV | NA | Hypertrophic cardiomyopathy, epileptic encephalopathy, methylglutaconic aciduria |
10 | 1–16 | F | lipidosis | N | No | Dilated cardiomyopathy, cerebellar ataxia |
11 | 1–16 | M | ↓ COX activity | ↓CIV | No | Hypotonia, hypertrophic cardiomyopathy, hyperlactatemia |
12 | 1–16 | M | NA | N (f) | No | Psychomotor delay, cerebellar ataxia, |
13 | 1–16 | M | NA | ↓CII and impaired assembly CII (f) | No | Psychomotor regression, spastic quadriparesis, leukodystrophy |
14 | 1–16 | F | COX- | N | No | Leigh syndrome without regression, encephalopathy, dystonia, hyperlactatemia |
15 | 1–16 | M | COX- | NA | NA | Myopathy |
16 | 1–16 | M | N | ↓CII, IV | No | Leigh syndrome with regression, epilepsy, ptosis |
17 | 1–16 | M | ↓COX activity lipidosis | N | No | Migraine, Stroke-like episodes, psychomotor delay |
18 | 1–16 | F | N | ↓CI, II, III, IV | No | Axonal neuropathy, cerebellar ataxia with cerebellar atrophy, deafness |
19 | 1–16 | M | N | ↓CI, IV | No | Psychomotor delay, moderate and late-onset Leigh syndrome, spastic paraparesia |
20 | 1–16 | F | lipidosis | N (m, f) | Yes | Episodic metabolic encephalopathy, deafness |
21 | 1–16 | M | COX- | N | Yes | Dilated cardiomyopathy, growth retardation, diabetes mellitus |
22 | 1–16 | M | COX- SDH- lipidosis | ↓CIV | No | Motor delay, refractory status epilepticus, regression, pyramidal and extrapyramidal syndrome |
23 | 1–16 | M | N | N, impaired assembly CIII (m), CV(l), N(f) | No | Stroke-like episodes, dystonia, myalgia, intellectual disability |
24 | 1–16 | F | NA | NA | NA | Fahr syndrome + clinical pseudostroke |
25 | > 16 | M | N | N (m, f, l) | No | Myoclonic epilepsy, ptosis |
26 | > 16 | M | N | ↓CIII | No | Cerebellar ataxia, stroke-like episodes |
27 | > 16 | F | N | ↓CII, III | No | Psychiatric disorder, distal weakness, vertical supranuclear gaze palsy, dystonia |
28 | > 16 | M | COX- lipidosis | N | No | Rhabdomyolysis |
29 | > 16 | F | N | NA | Yes | CPEO, sensorineural deafness, migraine |
30 | > 16 | F | NA | NA | NA | Optic atrophy |
31 | > 16 | M | NA | NA | NA | Optic atrophy |
32 | > 16 | F | RRF COX- | N | No | Sensorineural hypoacusia, CPEO, cachexia |
33 | > 16 | F | NA | N, impaired assembly CV | No | Leigh syndrome |
34 | > 16 | F | lipidosis | ↓CIII | No | Spinal muscular atrophy syndrome |
35 | > 16 | F | COX- | N | Yes | Sensory peripheral neuropathy, dysautonomia |
36 | > 16 | M | RRF COX- | N (f) | Yes | Ptosis, exercice intolerance, lipomatosis, dysphonia |
37 | > 16 | F | N | ↓CIII | Yes | Myalgia, exercise intolerance, diabetes, hypoacusia |
38 | > 16 | M | COX - | NA | Yes | Peripheral neuropathy, diabetes |
39 | > 16 | M | COX- | ↓CIII | NA | Myalgia, axial myopathy, ptosis |
40 | > 16 | M | NA | NA | NA | Optic atrophy |
41 | > 16 | F | N | ↓CII, III | Yes | Sensory ataxic neuropathy, optic neuropathy |
42 | > 16 | F | RRF COX- | NA | Single deletion | Kearn-Sayre Syndrome |
43 | > 16 | F | RRF COX- lipidosis | N | Yes | CPEO, motor-sensory demyelinating neuropathy |
44 | > 16 | F | NA | NA | NA | Diabetes, sensorineural deafness, pattern macular dystrophy, myalgia, nephropathy |
45 | > 16 | M | RRF Mitochondrial aggregates | NA | Yes | Cerebellar ataxia, dilated cardiomyopathy, peripheral neuropathy, renal insufficiency, deafness |
46 | > 16 | M | NA | NA | NA | Optic atrophy |
47 | > 16 | F | RRF lipidosis | N | Yes | Proximal myopathy, stroke-like episodes, psychiatric disorder, cognitive impairment |
48 | > 16 | F | lipidosis | N | Yes | Myalgia, exercise intolerance, rhabdomyolysis |
49 | > 16 | M | N | ↓CIII, IV, V | No | Axonal neuropathy, ophtalmoplegia, tremor, lipomatosis, deafness, cognitive impairment |
50 | > 16 | F | N | ↓CIII | Yes | CPEO |
51 | > 16 | F | NA | NA | NA | Bilateral optic atrophy |
52 | > 16 | M | N | ↓CII, III, IV | Yes | Exercise intolerance |
53 | > 16 | M | RRF COX- | N | Yes | Exercise intolerance, epilepsy, ptosis, peripheral neuropathy, extra-pyramidal syndrome |
54 | > 16 | F | RRF | NA | Single deletion | Ptosis, proximal myopathy |
55 | > 16 | M | RRF COX- lipidosis | NA | NA | Hypertrophic cardiomyopathy, hypoacusia, strokes |
56 | > 16 | F | RRF COX- | N | Yes | CPEO, deafness, proximal myopathy |
57 | > 16 | F | lipidosis | N | Yes | Axonal and sensory ataxic neuropathy, deafness, retinitis pigmentosa |
58 | > 16 | M | NA | NA | Diabetes, deafness | |
59 | > 16 | M | RRF COX- lipidosis | N | No | Myopathy, ptosis, dilated cardiomyopathy, dysphagia |
60 | > 16 | F | COX- lipidosis | N | No | Ptosis, myalgia, exercise intolerance |
61 | > 16 | M | COX- | N | Yes | Exercise intolerance, myalgia, rhabdomyolysis |
62 | > 16 | F | NA | NA | Diabetes, deafness, cerebellar ataxia, hypertrophic cardiomyopathy | |
63 | > 16 | M | NA | NA | No | Hypertrophic cardiomyopathy, deafness |
64 | > 16 | M | Mitochondrial aggregates | N | Yes | Cerebellar ataxia, CPEO |
65 | > 16 | F | COX- | NA | Yes | Dementia, axial myopathy, stroke-like episodes |
66 | > 16 | M | COX- | ↓CIV + impaired assembly CIV | No | CPEO, dysphagia |
67 | > 16 | M | COX- lipidosis | ↓CI | Yes | Cerebellar ataxia, myoclonic epilepsy, cataract, deafness, hyperlactatemia |
68 | > 16 | M | COX- | N | Yes | CPEO, dysphagia |
69 | > 16 | F | COX- | ↓CIII | Yes | Cerebellar syndrome, hepatic steatosis |
70 | > 16 | F | NA | NA | NA | CPEO, stroke-like episodes |
71 | > 16 | F | COX- | N | Yes | Axonal and sensory ataxic neuropathy, cachexia, deafness |
72 | > 16 | F | RRF COX- | ↓CI and quinones | Yes | Unilateral ptosis with familial history of autosomal dominant CPEO |
73 | > 16 | F | COX- | N | Yes | Myopathy |
74 | > 16 | F | NA | NA | NA | Sensory ataxic neuropathy, optic neuropathy, cognitive impairment, white matter hyperintensities |
75 | > 16 | F | RRF COX- | N | Yes | Axonal and sensory ataxic neuropathy, deafness, cardiac conduction block |
76 | > 16 | M | COX- | N | Yes | CPEO, ataxia |
77 | > 16 | M | COX- | hyperactivity CII, III, IV and CI + III, II + III | Yes | Peripheral neuropathy, fronto temporal dementia, Paget disease |
78 | > 16 | M | RRF COX- | N, impaired assembly CI | Yes | Axonal and sensory ataxic neuropathy, rhabdomyolysis |
79 | > 16 | M | COX- | N | Yes | CPEO, dysphagia, deafness |
80 | > 16 | M | RRF COX- | N | Yes | Ptosis, dysphagia, cerebellar ataxia, hypoacusia, exercise intolerance |
Molecular genetics
mtDNA analysis
Custom targeted panel analysis
Validation of variants identified by NGS
Results
Analysis of the mitochondrial genome
Patient N° | Age-range onset (years) / sex | Pathogenic variant | Tissue | Clinical presentation |
---|---|---|---|---|
24 | 1–16 / F | m.1555A > G homoplasmic | blood, urine | Fahr syndrome + clinical pseudostroke |
28 | > 16 / M | m.3243A > G heteroplasmic | muscle | Rhabdomyolysis |
30 | > 16 / F | m.3460G > A homoplasmic | blood | Optic atrophy |
31 | > 16 / M | m.11178G > A homoplasmic | blood | Optic atrophy |
32 | > 16 / F | m.5703G > A heteroplasmic | urine, buccal | Sensorineural hypoacusia, CPEO, cachexia |
33 | Infancy / F | m.8993 T > C homoplasmic | muscle | Leigh syndrome |
40 | > 16 / M | m.11178G > A homoplasmic | blood | Optic atrophy |
42 | > 16 / F | Single deletion | muscle | Kearn-Sayre Syndrome |
44 | > 16 / F | m.3243A > G heteroplasmic | buccal, blood | Diabetes, sensorineural deafness, pattern macular dystrophy, myalgia, nephropathy |
46 | > 16 / M | m.11178G > A homoplasmic | blood | Optic atrophy |
54 | > 16 / F | Single deletion | muscle | Ptosis, proximal myopathy |
55 | > 16 / M | m.3243A > G heteroplasmic | blood, muscle | Hypertrophic cardiomyopathy, hypoacusia, strokes |
58 | > 16 / M | m.1555A > G heteroplasmic | blood | Diabetes, deafness |
62 | > 16 / F | m.3243A > G heteroplasmic | blood, urine | Diabetes, deafness, cerebellar ataxia, hypertrophic cardiomyopathy |
63 | > 16 / M | m.3243A > G heteroplasmic | blood | Hypertrophic cardiomyopathy, deafness |
Analysis of the nuclear genome
Pathogenic variants
Patient N° | Age-ranges onset (years) / sex | Gene | Nucleotide change | Protein change | Trait | Concordant phenotype | ExAC frequency | SIFT score | Polyphen 2 | Variant reported | Notes | References |
---|---|---|---|---|---|---|---|---|---|---|---|---|
6 | NN / F |
AGK
| c.412C > T / c.412C > T | p.Arg138* | AR | Yes | 0 | NA | NA | Yes | Csg; parents: htz | Mayr et al., 2012 [36] |
7 | NN / M |
ETHE1
| c.608C > T / c.554 T > G | p.Ser203Phe / p.Leu185Arg | AR | Yes | < 0.01% < 0.01% | 0.0 0.0 | 0.975 1 | No Yes | Parents: htz | Tiranti et al., 2005 [37] |
10 | NN / F |
DNAJC19
| c.51delT / c.51delT | p.Phe17Leufs*10 | AR | Yes | 0 | NA | NA | No | – | – |
13 | 1–16 / M |
SDHAF1
| c.164G > C / c.164G > C | p.Arg55Pro | AR | Yes | 0 | 0.0 | 1.0 | Yes | Parents: htz | Ghezzi et al., 2009 [38] |
15 | 1–16 / M |
TK2
| c.343C > T / c.323C > T | p.Leu115Phe / p.Thr108Met | AR | Yes | 0 < 0.01% | 0.0 0.2 | 1 1 | No Yes | Parents: htz | Béhin et al., 2012 [39] |
29 | > 16 / F |
TWNK
| c.1363A > G | p.Met455Val | AD | Yes | 0 | 0.0 | 0.996 | No | – | – |
43 | > 16 / F |
TYMP
| c.1112 T > C / c.1112 T > C | p.Leu371Pro | AR | Yes | 0 | 0.18 | 0.999 | Yes | – | Kocaefe et al., 2003 [40] |
68 | > 16 / M |
OPA1
| c.1892_1893delAT | p.His631Argfs*3 | AD | Yes | 0 | NA | NA | Yes | – | Ferré et al., 2009 [41] |
Variants of uncertain significance (VUS)
Patient N° | Age-ranges onset (years) / sex | Gene | Nucleotide change | Protein change | Trait | Concordant phenotype | ExAC frequency | SIFT score | Polyphen 2 | Variant reported | Notes | References |
---|---|---|---|---|---|---|---|---|---|---|---|---|
34 | 1–16 / F |
KIF1B
| c.4682G > A | p.Cys1561Tyr | AD | Yes | < 0.01% | 0.02 | 0.987 | No | – | – |
35 | > 16 / F |
POLG2
| c.390-2A > C | – | AD | Yes | 1 | – | – | No | + c.1105A > G htz (polymorphism) | – |
64 | > 16 / M |
SYNE1
| c.23315G > A / c.15337G > A | p.Arg7772Gln / p.Val5113Ile | AR | Yes | < 0.01% < 0.01% | 0.01 0.29 | 0.956 0.968 | No Yes | c.15337G > A htz (patient’s daughter) | Neubauer et al., 2017 [17] |
66 | 1–16 / M |
AIFM1
| c.893G > A | p.Arg298Gln | X-linked | +/− | < 0.01% | 0.63 | 0.402 | No | Mild phenotype | Ardissone et al., 2015 [9] |
67 | > 16 / M |
DNA2
| c.2862G > C | p.Leu954Phe | AD | Yes | 0 | 0.0 | 0.669 | No | Severe phenotype | – |
71 | > 16 / F |
KIF5A
| c.1248A > T | p.Lys416Asn | AD | Yes | 0 | 0.01 | 0.935 | No | – | – |
77 | > 16 / M |
KIF5A
| c.2354A > G | p.Glu785Gly | AD | Yes | 0 | 0.0 | 0.999 | No | – | – |
Misannotated mutations and likely benign variants
Patient N° | Age onset (years) / sex | Gene | Nucleotide change | Protein change | Trait | Concordant phenotype | ExAC frequency | SIFT score | Polyphen 2 | Variant reported | Notes | References |
---|---|---|---|---|---|---|---|---|---|---|---|---|
2 | NN / F |
PC
| c.715A > G /? | p.Ile239Val | AR | No | < 0.01% | 0.28 | 0.04 | No | – | |
22 | 1–16 / M |
OPA3
| c.229G > A /? | p.Ala77Thr | AD / AR | No | 0 | 0.12 | 1.0 | No | Mother: htz | – |
23 | 1–16 / M |
MFN2
| c.1987C > T | p.Arg663Cys | AD | No | < 0.01% | 0.0 | 1.0 | Yes | Di Meglio et al., 2016 [19] | |
52 | > 16 / M |
MFN2
| c.1085C > T | p.Thr362Met | AD | No | < 0.01% | 0.0 | 1.0 | Yes | Chung et al., 2006 [42] | |
59 | > 16 / M |
MLYCD
| c.206C > T /? | p.Ala69Val | AR | No | < 0.01% | 0.07 | 0.685 | Yes | Wightman et al., 2003 [24] | |
69 | > 16 / F |
DGUOK
| c.750G > T /? | p.Leu250Phe | AR | No | 0 | 0.0 | 1.0 | No | – |