Case# F2:II.2, F, 5mo onset, Turkey

CasePresentingHPOs HP:0001263, HP:0006846, HP:0003201, HP:0011675, HP:0002925, HP:0100543, HP:0001250, HP:0002061, HP:0012444, HP:0001943, HP:0002151, HP:0002919, HP:0045045, HP:0040145, HP:0001270, HP:0001259, HP:0003236, HP:0000648

HPOcont: Global developmental delay, Acute encephalopathy, Rhabdomyolysis, Arrhythmia, Elevated TSH, Cognitive impairment, Seizures, Lower limb spasticity, Brain atrophy, Hypoglycemia, Elevated lactate, Ketonuria, Elevated acylcarnitine, Dicarboxylic acidemia, Motor delay, Coma, Elevated CK, Optic atrophy

HPOFreeText: "starting from the age of five months, psychomotor development appeared delayed. At the age of one year, spasticity predominantly involving the legs was noted. Nevertheless, the child was relatively active and was able to sit and crawl. However, after an episode of infection, she lost already acquired skills. Laboratory investigations during this episode showed transiently elevated CK activity (up to 2,970 U/l; NR < 269 U/l). At the age of 15 months, the girl suffered from a febrile upper airway infection during which she suddenly became comatose."

CasePreviousTesting "Sequence analysis of the mitochondrial DNA and CPT2 did not show clinically relevant variants. Laboratory investigations revealed hypoglycemia (31 mg/dl; NR >50 mg/dl) and severe lactic acidosis (lactate up to 16.6 mmol/L; NR < 2.1 mmol/L). Biochemical analysis of fresh muscle tissue showed moderately reduced ATP production rate and a mildly reduced activity of mitochondrial complex I. Brain MRI demonstrated mild global brain atrophy without focal abnormalities. Eye examination showed bilateral optic atrophy. Acylcarnitine profiling showed normal free carnitine concentrations in dried blood while C14:1 acylcarnitine was mildly elevated (0.31 μmol/L; NR 0-0.25 μmol/L). Analysis of organic acids in urine revealed increased concentrations of dicarboxylic acids and ketone bodies as well as massive excretion of lactate." Then at 12 years, elevated TSH concentration (7.17 μIU/ml; NR 0.28-4.31 μIU/ml).

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES, confirmed with Sanger in patient and parents

Variant NM_001283106.2(TANGO2):c.418C>T (p.Arg140Ter)

ClinVar 224774

CAID CA358667

gnomAD 1.501e-05(European (Non-Finnish)), 8.254e-06(Total)

VariantEvidence (Figure 3) In assessment of Palmitate-Dependent Mitochondrial Respiration, oxygen consumpition rates were decreased in patient fibroblasts by ~20% compared to control.

CaseAddInfo "measurement of pyruvate-dependent oxygen consumption rates in fibroblast cell lines from individuals F1:II.2 and F2:II.2 was unremarkable." consanguineous parents, healthy older sibling

CasePMIDs n/a

Case# F1:II.2, F, 2yo onset, European

CasePresentingHPOs HP:0001263, HP:0006846, HP:0003201, HP:0011675, HP:0002925, HP:0001250, HP:0012444, HP:0001943, HP:0002151, HP:0045045, HP:0040145, HP:0001259, HP:0002133, HP:0002913, HP:0003128, HP:0002061, HP:0001664, HP:0008936, HP:0001344, HP:0000252, HP:0003236, HP:0001946, HP:0100543

HPOcont: Global developmental delay, Acute encephalopathy, Rhabdomyolysis, Arrhythmia, Elevated TSH, Seizures, Brain atrophy, Hypoglycemia, Elevated lactate, Elevated acylcarnitine, Dicarboxylic acidemia, Coma, Status epilepticus, Myoglobinuria, Lactic acidosis, Lower limb spasticity, Torsade de pointes, Trunk hypotonia, Absent Speech, Microcephaly, Elevated CK, Ketosis, Cognitive Impariment

HPOFreeText: "At the age of 2 7/12 years, she suffered from an infection and suddenly became comatose with status epilepticus. Her renal function was transiently impaired due to massive rhabdomyolysis with myoglobinuria. The girl’s condition subsequently improved but she was unable to sit due to truncal hypotonia. She developed progressive spasticity in the legs, and communicated only non-verbally. Two months later a second episode occurred, which was again triggered by an infection and presented with similar clinical and laboratory findings. A third metabolic decompensation with lactic acidosis, hypoglycemia and rhabdomyolysis occurred six weeks later. This time, additional cardiac involvement with long QT syndrome and torsade de pointes tachyarrhythmia required intensive care treatment and implantation of a cardioverter-defibrillator (ICD) device. Seizures occurred which were responsive to antiepileptic medication. The girl remained with severely impaired psychomotor capabilities, marked truncal muscular hypotonia, moderate spasticity in the lower limbs, dystonic movements in the upper limbs, absent speech, and impaired social interaction. Secondary microcephaly became evident (head circumference < P3)."

CasePreviousTesting "marked hypoglycemia (18 mg/dl; normal range (NR) > 50 mg/dl). Initial laboratory testing documented massively elevated plasma creatine kinase (CK) activity (maximum 300,000 U/l, NR < 227 U/l) as well as elevated plasma lactate concentrations up to 3.8 mmol/l (NR < 1.6 mmol/l). Urine organic acid analyses during crises showed a massive excretion of ketone bodies (around 2,000 mmol/mol creatinine), lactate (2,000 mmol/mol creatinine; NR < 285 mmol/mol creatinine), and dicarboxylic acids (values given in mmol/mol creatine: adipic (1,513; NR < 34), glutaric (24; NR = not detectable), sebacic (712; NR < 1.4), suberic (494; NR < 10), decenedioic (581; NR = not detectable), and of note malonic (145; NR = not detectable) acid). Acylcarnitine profiling in dried blot spots collected during the crisis showed free carnitine concentrations within normal ranges while several acylcarnitines were elevated 2-5-fold above the respective normal range (i.e. C5DC, C6DC, C10:1, C12, C12:1, C14:1, C14:2). In addition, an elevated TSH concentration (16.6 mU/l; NR 0.5-4.5 mU/l) was detected and treatment with L-thyroxine was initiated. Targeted sequencing of CPT2, ETFA, ETFB, ETFDH, and GCDH did not reveal clinically relevant variants."

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES, confirmed with Sanger in patient and parents

Variant (1) NM_001283106.2(TANGO2):c.4delT (p.Cys2Alafs) (2) NM_152906.5:c.(56+1_57-1)(*1?)del

ClinVar (1) 224773

CAID (1) CA358861

gnomAD n/a

CaseAddInfo "measurement of pyruvate-dependent oxygen consumption rates in fibroblast cell lines from individuals F1:II.2 and F2:II.2 was unremarkable." Healthy twin brother.

CasePMIDs n/a

Case# Subject 5, F, 7yo onset, Hispanic

CasePresentingHPOs HP:0001270, HP:0000750, HP:0005184, HP:0001250, HP:0008942, HP:0003236, HP:0001664, HP:0004756, HP:0011675, HP:0001943, HP:0002151, HP:0003201, HP:0001249, HP:0002913, HP:0003324, HP:0001695, HP:0006956

HPOcont: Motor Delay, Speech Delay, Prolonged QTc interval, Seizures, Elevated CPK, Torsade de pointes, Ventricular tachycardia, Arrhythmia, Hypoglycemia, Elevated Lactate, Acute rhabdomyolysis, Intellectual Disability, Myoglobinuria, Generalized Muscle Weakness, Cardiac Arrest, Enlarged lateral ventricles

HPOFreeText: speech and motor delay, prolonged QTc interval, seizures, prior to her acute presentation. (7 years) acute rhabdomyolysis, high CPK and myoglobinuria. (13 years) muscle weakness, cardiac arrest, torsade de pointes from prolonged QTc interval, ventricular tachycardia with recurrent pulseless arrest and arrhythmia, able to ambulate.

CaseNotHPOs n/a

CasePreviousTesting highest CPK (60,000 U/L), 953 U/L for AST, 540 U/L for ALT, and CPK-MB of 291 U/L.

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES and cSNP results confirmed with Sanger

Variant (1) NM_152906.6:c.460G>A (p.Gly154Arg)

ClinVar (1) 208823

CAID (1) CA358646

gnomAD (1) 0.001549(Other), 0.0001208(Overall)

VariantEvidence (Figure 3) using "EBV-transformed B-lymphoblastoid cell lines (BLCLs) from another individual, subject 4 with homozygous c.460G>A (p.Gly154Arg) mutation, and evaluated the Golgi by intracellular staining with WGA, as well as cis Golgi marker, anti-GM130 antibody." WGA stain resolved lower area of golgi bodies in p.Gly154Arg cells than WT. Measured immunoglobulin heavy chain binding protein levels in WT and and patient fibroblasts, BiP levels in patient cells lower than WT after ER induced stress by Brefeldin A.

CaseAddInfo nonconsanguineous, parents confirmed heterozygotes

CasePMIDs n/a

Lalani, 2016 (AJHG article)

9 cases (5 scored)

NM_152906.6:c.460G>A (p.Gly154Arg)

exons 3-9del

exons 4-6del can be registered (which chr.22 transcript does this paper use? NM_152906.5 does not line up in NC_000022.11 (tested by Courtney))

Case# Subject 1, F, 4yo onset, Hispanic

CasePresentingHPOs HP:0002373, HP:0001260, HP:0006957, HP:0002913, HP:0007359, HP:0002104, HP:0003236, HP:0001987, HP:0001943, HP:0002058, HP:0000252, HP:0006801, HP:0003487, HP:0000577, HP:0002376, HP:0003236, HP:0001249, HP:0003201, HP:0000252

HPOcont: Febrile seizures, Dysarthria, loss of ability to walk, Myoglobinuria, Focal autonomic seizures, Apnea, Hyperammonemia, Hypoglycemia, Myopathic facies, Microcephaly, Brisk DTR, Babinski sign, Exotropia, Developmental regression, Elevated CPK, Hypoglycemia, Intellectual Disability, Rhabdomyolysis, Microcephaly

HPOFreeText: Febrile seizure at 1 year of age, developmental regression in the following 3 years with recurrent seizures, losing the ability to ambulate and speak, as well as right focal seizure, apnea, and unresponsiveness triggered by fever. On hospital admission she was noted to have elevated urine myoglobin, elevated creatine phosphokinase, aspartate aminotransferase, alanine aminotransferase, ammonia and hypoglycemia. MRI showed mild diffuse atrophy of the left cerebral hemisphere. "Ophthalmology evaluation showed intermittent exotropia. Echocardiogram and electrocardiogram (ECG) were unremarkable. Hysical examination was relevant for microcephaly (FOC 47.5 cm; <5th percentile for age), myopathic facies with drooling, increased tone in all extremities, and brisk deep tendon reflexes (DTRs) throughout with positive Babinski sign.

CaseNotHPOs HP:0011675

NotHPOcont: Arrhythmia

CasePreviousTesting "urine myoglobin of 94 ng/ml (normal range 10–65 ng/ml), serum creatine phosphokinase (CPK) of 205,000 U/l (normal range 75–230 U/l), elevated aspartate aminotransferase (AST) of 1,618 U/l (normal range 15–50 U/l), alanine aminotransferase (ALT) of 571 U/l (normal range 10–25 U/l), ammonia of 122 μmol/l (normal range 22–48 μmol/l), and hypoglycemia (blood glucose 30 mg/dl; normal range 70–110 mg/dl)."

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES and cSNP results confirmed with Sanger

Variant (1) NM_152906.6:c.460G>A (p.Gly154Arg)

ClinVar (1) 208823

CAID (1) CA358646

gnomAD (1) 0.001549(Other), 0.0001208(Overall)

VariantEvidence (Figure 3) using "EBV-transformed B-lymphoblastoid cell lines (BLCLs) from another individual, subject 4 with homozygous c.460G>A (p.Gly154Arg) mutation, and evaluated the Golgi by intracellular staining with WGA, as well as cis Golgi marker, anti-GM130 antibody." WGA stain resolved lower area of golgi bodies in p.Gly154Arg cells than WT. Measured immunoglobulin heavy chain binding protein levels in WT and and patient fibroblasts, BiP levels in patient cells lower than WT after ER induced stress by Brefeldin A.

CaseAddInfo nonconsanguineous, mother tested heterozygous, father unavailable. cSNP data showed no evidence of deletion or uniparental isodisomy of the region.

CasePMIDs n/a

Case# Subject 4, M, 8yo onset, Hispanic

CasePresentingHPOs HP:0001249, HP:0001289, HP:0002066, HP:0009053, HP:0007340, HP:0001987, HP:0002925, HP:0005184, HP:0002058, HP:0002169, HP:0003201, HP:0001250, HP:0003236, HP:0000821, HP:0006801

HPOcont: Intellectual Disability, Confusion, Gait ataxia, Lower limb muscle weakness, Dysarthria, Hyperammonemia, Elevated TSH, Prolonged QTc interval, Myopathic facies, Clonus, Rhabdomyolysis, Seizures, Elevated CPK, Hypothyroidism, Brisk DTR

HPOFreeText: (2 years) uncoordinated gait and intellectual disability. (8 years) disorientation, ataxic gait, weakness in lower extremities, and dysarthria. (12 years) myopathic facies, brisk tendom reflexes, clonus, and impaired gait.

CaseNotHPOs HP:0001943, HP:0002151, HP:0002913

NotHPOcont: Hypoglycemia, Elevated Lactate, Myoglobinuria

CasePreviousTesting "lactate and glucose normal; elevated ammonia(111 μmol/l), elevated CPK (16,674 U/l). Urine was negative for myoglobin. TSH level was increased to 30.8 μIU/ml (range 0.32–5.00 μIU/ml), T3 was 166 ng/dl (range 90–260 ng/dl), and T4 was 5.2 μg/dl (range 6.4–13.3 μg/dl). Urine organic acids were normal."Muscle biopsy showed normal respiratory chain studies. Mitochondrial genome sequencing for common point mutations and deletions were normal."

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES and cSNP results confirmed with Sanger

Variant (1) NM_152906.6:c.460G>A (p.Gly154Arg)

ClinVar (1) 208823

CAID (1) CA358646

gnomAD (1) 0.001549(Other), 0.0001208(Overall)

VariantEvidence (Figure 3) using "EBV-transformed B-lymphoblastoid cell lines (BLCLs) from subject 4 with homozygous c.460G>A (p.Gly154Arg) mutation, and evaluated the Golgi by intracellular staining with WGA, as well as cis Golgi marker, anti-GM130 antibody." WGA stain resolved lower area of golgi bodies in p.Gly154Arg cells than WT. Measured immunoglobulin heavy chain binding protein levels in WT and and patient fibroblasts, BiP levels in patient cells lower than WT after ER induced stress by Brefeldin A.

CaseAddInfo nonsanguineous, confirmed heterozygosity of both parents

CasePMIDs n/a

Case# Subject 2, F, 6mo onset, Hispanic/European

CasePresentingHPOs HP:0001942, HP:0003128, HP:0002919, HP:0001987, HP:0002094, HP:0006682, HP:0004756, HP:0045045, HP:0001288, HP:0002013, HP:0007340, HP:0002913, HP:0002058, HP:0002307, HP:0001260, HP:0001251, HP:0003201, HP:0002151, HP:0001249, HP:0001943, HP:0003236, HP:0005184, HP:0002910, HP:0012544, HP:0006956, HP:0100960, HP:0001254

HPOcont: Metabolic acidosis, Lactic acidosis, Ketonuria, Hyperammonemia, Dyspnea, Ventricular extrasystoles, Ventricular tachycardia, Elevated acylcarnitine, Gait abnormality, Emesis, Lower limb muscle weakness, Myoglobinuria, Myopathic facies, Drooling, Dysarthria, Ataxia, Rhabdomyolysis, Elevated Lactate, Intellectual Disability, Hypoglycemia, Elevated CPK, Prolonged QTc interval, Elevated Transaminases, Elevated aldolase, Lateral ventrical dilation, Asymmetric ventricles, Lethargy

HPOFreeText: (6 months) metabolic acidosis, lactic acidemia, ketonuria, elevated blood ammonia and Kussmaul breathing, in addition to prolonged QTc interval, premature ventricular contractions just short of ventricular tachycardia, and elevated acycarnitine profile. (16 months) gait abnormality, weakness, sore troat, and vomiting. (5 years) after infection, lethargy, lower limb weakness, myoglobinuria, elevated CPK, transaminases, lactate, and aldolase in additon to myopathic face, drooling, dysarthric speech and ataxia.

CaseNotHPOs HP:0001250

NotHPOcont: Seizures

CasePreviousTesting "metabolic acidosis (pH of 7.0; base deficit of 20 mEq/l) and lactic acidemia of 15 mmol/l (normal range 0.2–2.0 mmol/l), serum ammonia was mildly elevated to 138 μmol/l. Acylcarnitine profile showed a primary peak of C14:1 in addition to C14:2, C16, C18, and some hydroxy derivatives." At 15 months of age "CPK of 1,126 U/l, AST of 158 U/L, mildly elevated ammonia of 71 μmol/l, and lactate of 7.0 mmol/l, then at 5 years, CPK of 287,230 U/l, hypoglycemia (glucose of 17 mg/dl), elevated transaminases (AST of 7,618 U/l and ALT of 2,564 U/l), lactate was 2.0 mmol/l, aldolase level was 595 U/l (normal range 2.7–8.8 U/l). Renal function tests remained stable throughout admission. Etiologic evaluations, including DNA sequencing of ACADVL for VLCAD deficiency, muscle histopathology, quantitative mtDNA studies in muscle, and mitochondrial genome sequencing for common point mutations and deletions, were normal."

CaseMethod1 WES

CaseMethod2 PCR

CaseGenotypingMethod WES and cSNP array, validated deletion variant with PCR

Variant (1) NM_152906.6:c.460G>A (p.Gly154Arg), (2) ~34kb, exon3-9del

ClinVar (1) 208823

CAID (1) CA358646

gnomAD (1) 0.001549(Other), 0.0001208(Overall)

VariantEvidence (1)(Figure 3) using "EBV-transformed B-lymphoblastoid cell lines (BLCLs) from another individual, subject 4 with homozygous c.460G>A (p.Gly154Arg) mutation, and evaluated the Golgi by intracellular staining with WGA, as well as cis Golgi marker, anti-GM130 antibody." WGA stain resolved lower area of golgi bodies in p.Gly154Arg cells than WT. Measured immunoglobulin heavy chain binding protein levels in WT and and patient fibroblasts, BiP levels in patient cells lower than WT after ER induced stress by Brefeldin A.

CaseAddInfo nonconsanguineous, found deletion variant in with PCR father and mother carried missense

CasePMIDs n/a

Case# Subject 6, M, 1yo onset, Hispanic

CasePresentingHPOs HP:0001263, HP:0002098, HP:0002013, HP:0001943, HP:0001942, HP:0002151, HP:0001290, HP:0001987, HP:0001249, HP:0001946, HP:0045045, HP:0040145, HP:0001508, HP:0003648

HPOcont: Global developmental delay, Respiratory Distress, Emesis, Hypoglycemia, Metabolic acidosis, Elevated Lactate, Generalized hypotonia, Hyperammonemia, Intellectual Disability, Ketosis, Elevated acylcarnitine, Dicarboxylic acidemia, Failure to thrive, Lacticaciduria

HPOFreeText: (1 year) developmental delay, emesis, difficulty breathing, elevate metabolites, elevated urine organic acids, elevations of 3-hydroxy-N-butyric and acetoacetic acids (ketone bodies), as well as adipic, suberic, sebacic, and 3-hydroxysebacic (dicarboxylic) acids. Found to also have a head circumference in 6th percentile and hypotonia.

CaseNotHPOs HP:0001250, HP:0011675, HP:0003201

NotHPOcont: Seizures, Arrhythmia, Rhabdomyolysis

CasePreviousTesting Tested blood gas pH (7.1), serum bicarbonate(16 mEq/L (normal range 22-28 mEq/L)), serum lactate(11.7 mmol/L), serum ammonia( 102 μmol/L), elevated very long chain acylcarnitine species, especially C14, normal serum CPK. Chromosomal microarray and Fragile X results were normal.

CaseMethod1 WES

CaseMethod2 n/a

CaseGenotypingMethod WES and cSNP array

Variant NM_152906.6(TANGO2):c.605+1G>C

ClinVar 521699

CAID CA358646

VariantEvidence splice site

CaseAddInfo consanguineous parents

CasePMIDs n/a

Case# Subject 3, F, 5mo onset, Hispanic

CasePresentingHPOs HP:0002910, HP:0001942, HP:0003201, HP:0001664, HP:0002878, HP:0001663, HP:0001249, HP:0001250, HP:0008619, HP:0100295, HP:0001260, HP:0004756, HP:0001259, HP:0012734, HP:0002151, HP:0003236, HP:0002307, HP:0000252, HP:0004322, HP:0004325, HP:0002058, HP:0002136

HPOcont: Elevated Transaminases, Metabolic acidosis, Rhabdomyolysis, Torsade de pointes, Respiratory Failure, Ventricular fibrillation, Intellectual Disability, Seizures, Bilateral sensorineural hearing impairment, Muscle fiber atrophy, Dysarthria, Ventricular tachycardia, Coma, Ketotic hypoglycemia, Elevated Lactate, Elevated CPK, Drooling, Microcephaly, Short Stature, Low body weight, Myopathic facies, Broad-based gait

HPOFreeText: (5 months) coma, metabolic acidosis and rhabdomyolysis. (24 years) torsade de pointes, respiratory and multiorgan failure, ventricular fibrillation, epilepsy, bilateral sensorineural hearing loss, intellectual disability and atrophic muscle fibers. She was ambulatory, some speech, drooling, myopathic facies, and wide-based gait. "Height and weight below the 5th percentile for age (weight 42.9 kg, height 147 cm), head circumference below 5th percentile for age (51.4 cm)."

CaseNotHPOs HP:0002540, HP:0001987

NotHPOcont: Non-ambulatory, Hyperammonemia

CasePreviousTesting CPK elevated to 8,000 U/I on first episode, then 22,000 U/I during most severe episode.

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES and cSNP results confirmed with Sanger

Variant (1) NM_152906.6:c.460G>A (p.Gly154Arg)

ClinVar (1) 208823

CAID (1) CA358646

gnomAD (1) 0.001549(Other), 0.0001208(Overall)

VariantEvidence (Figure 3) using "EBV-transformed B-lymphoblastoid cell lines (BLCLs) from another individual, subject 4 with homozygous c.460G>A (p.Gly154Arg) mutation, and evaluated the Golgi by intracellular staining with WGA, as well as cis Golgi marker, anti-GM130 antibody." WGA stain resolved lower area of golgi bodies in p.Gly154Arg cells than WT. Measured immunoglobulin heavy chain binding protein levels in WT and and patient fibroblasts, BiP levels in patient cells lower than WT after ER induced stress by Brefeldin A.

CaseAddInfo nonconsanguineous, parents confirmed heterozygotes

CasePMIDs n/a