Comprehensive Metabolism Panel

  • bpg-method PLUS
  • bpg-method SEQ
  • bpg-method DEL/DUP

Test code: ME0701

The Blueprint Genetics Comprehensive Metabolism Panel is a 354 gene test for genetic diagnostics of patients with clinical suspicion of inborn error of metabolism.

Most inborn errors of metabolism are inherited in autosomal recessive manner. However, also autosomal dominant as well as X-linked types of inheritance are possible. This Panel includes Aicardi-Goutieres Syndrome Panel, Coenzyme q10 Deficiency Panel, Congenital and Familial Lipodystrophy Panel, Congenital Disorders of Glycosylation Panel, Creatine Metabolism Deficiency Panel, Cystinuria Panel, Fatty Acid Oxidation Syndrome Panel, Glucogen Storage Disorder Panel, Hereditary Hemochromatosis Panel, Hyperammonemia and Urea Cycle Disorder Panel, Hypoglycemia, Hyperinsulinism and Ketone Metabolism Panel, Hyperphenylalaninemia Panel, Hypomagnesemia Panel, Lysosomal Disorders and Mucopolysaccharidosis Panel, Metabolic Myopathy and Rhabdomyolysis Panel, Mitochondrial DNA Depletion Syndrome Panel, Organic Acidemia and Acidurina and Cobalamin Deficiency Panel, Periodic Paralysis Panel, Peroxisomal Disorder Panel and Porphyria Panel.

About Metabolic Diseases

Metabolic disorders often have similar and overlapping symptoms. They may be difficult to subtype without definitive information on the causative mutations and genes. This Panel includes well over 300 genes – comprehensively enough to cover most of all known monogenic metabolic syndromes, deficiencies and diseases. Most phenotypes covered by this Panel result from mutations making specific enzymes defective in metabolic pathways. This results often in an accumulation of toxic intermediate products or loss of specific end products required in metabolic pathways. Additionally, conditions covered include those with imbalance in using, storing or converting energy.

Most inherited metabolic disorders are quite rare. However, considering them all together, the combined prevalence is estimated at 1:1000 or 1:2000 newborns. Some specific populations, where the genetic heterogeneity is smaller, may even have much higher numbers.

Availability

Results in 3-4 weeks. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more: http://blueprintgenetics.com/faqs/#prenatal

Genes in the Comprehensive Metabolism Panel and their clinical significance
Gene Associated phenotypes Inheritance ClinVar HGMD
ABCC8 Hyperinsulinemic hypoglycemia, Diabetes, permanent neonatal, Hypoglycemia, leucine-induced, Diabetes mellitus, transient neonatal AD/AR 122 613
ABCD1* Adrenoleukodystrophy XL 64 658
ABCD4 Methylmalonic aciduria and homocystinuria AR 5 7
ACAA1 Pseudo-Zellweger syndrome AD/AR
ACAD9 Acyl-CoA dehydrogenase family, deficiency AR 23 42
ACADL Long chain acyl-CoA dehydrogenase deficiency AD/AR
ACADM Acyl-CoA dehydrogenase, medium chain, deficiency AR 84 166
ACADS Acyl-CoA dehydrogenase, short-chain, deficiency AR 50 81
ACADVL Acyl-CoA dehydrogenase, very long chain, deficiency AR 94 260
ACAT1 Alpha-methylacetoacetic aciduria AR 32 76
ACOX1 Peroxisomal acyl-CoA oxidase deficiency AR 13 25
ACSF3 Combined malonic and methylmalonic aciduria AR 19 19
ACY1 Aminoacylase 1 deficiency AR 5 14
ADAMTSL2 Geleophysic dysplasia AR 8 27
ADAR Dyschromatosis symmetrica hereditaria, Aicardi-Goutières syndrome AD/AR 21 205
ADCK3 Coenzyme Q10 deficiency, Progressive cerebellar ataxia and atrophy, Spinocerebellar ataxia AR 40 37
ADSL Adenylosuccinase deficiency AR 24 56
AGA Aspartylglucosaminuria AR 40 36
AGK* Sengers syndrome AR 15 21
AGL Glycogen storage disease AR 82 242
AGPAT2 Lipodystrophy, congenital generalized AR 25 38
AKT2 Hypoinsulinemic hypoglycemia with hemihypertrophy AD 4 3
ALAD Porphyria, acute hepatic AR 7 11
ALAS2 Anemia, sideroblastic, Protoporphyria, erythropoietic XL 26 94
ALDH5A1 Succinic semialdehyde dehydrogenase deficiency AR 10 69
ALDH7A1 Epilepsy, pyridoxine-dependent AR 43 112
ALDOA Glycogen storage disease AR 2 8
ALG1* Congenital disorder of glycosylation AR 20 41
ALG2 Congenital disorder of glycosylation, Myasthenic syndrome, congenital AR 4 4
ALG3 Congenital disorder of glycosylation AR 7 14
ALG6 Congenital disorder of glycosylation AR 8 24
ALG8 Congenital disorder of glycosylation AR 9 15
ALG9 Congenital disorder of glycosylation AR 3 4
ALG11 Congenital disorder of glycosylation AR 11 14
ALG12 Congenital disorder of glycosylation AR 9 14
ALG13 Congenital disorder of glycosylation XL 5 7
AMACR Alpha-methylacyl-CoA racemase deficiency, Bile acid synthesis defect AR 3 8
AMT Glycine encephalopathy AR 26 95
ANO10 Spinocerebellar ataxia AR 15 16
ANTXR2 Hyalinosis, infantile systemic, Fibromatosis, juveline hyaline AR 16 43
APTX Ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia AR 14 40
ARG1 Hyperargininemia AR 16 54
ARSA Metachromatic leukodystrophy AR 92 215
ARSB Mucopolysaccharidosis (Maroteaux-Lamy) AR 22 196
ASAH1 Spinal muscular atrophy with progressive myoclonic epilepsy, Farber lipogranulomatosis AR 11 56
ASL Argininosuccinic aciduria AR 35 153
ASPA Aspartoacylase deficiency (Canavan disease) AR 37 102
ASS1 Citrullinemia AR 52 153
ATP6V0A2 Cutis laxa, Wrinkly skin syndrome AR 16 53
ATP13A2 Parkinson disease (Kufor-Rakeb syndrome) AR 17 37
AUH 3-methylglutaconic aciduria AR 13 11
B3GLCT Peters-plus syndrome AR 8 15
B4GALT1 Congenital disorder of glycosylation AR 1 2
BCKDHA Maple syrup urine disease AR 42 91
BCKDHB Maple syrup urine disease AR 65 94
BSCL2 Lipodystrophy, congenital generalized, Encephalopathy, progressive AR 29 46
BTD Biotinidase deficiency AR 183 235
C10ORF2 Perrault syndrome, Mitochondrial DNA depletion syndrome AR 37
C12ORF65 Spastic paraplegia, Combined oxidative phosphorylation deficiency AR 10 10
CACNA1S Hypokalemic periodic paralysis, Malignant hyperthermia, Thyrotoxic periodic paralysis AD 7 40
CAV1 Partial lipodystrophy, congenital cataracts, and neurodegeneration syndrome, Lipodystrophy, congenital generalized AD/AR 7 9
CAV3 Creatine phosphokinase, elevated serum, Hypertrophic cardiomyopathy (HCM), Long QT syndrome AD/Digenic 24 48
CBS Homocystinuria due to cystathionine beta-synthase deficiency AR 69 187
CD320 Methylmalonic aciduria due to transcobalamin receptor defect AR
CKMT1A* AD/AR
CKMT1B* AD/AR 1
CKMT2 AD/AR
CLCN1 Myotonia congenita, Myotonia congenita, Myotonia levior AD/AR 55 295
CLDN16 Hypomagnesemia, renal AR 18 61
CLDN19 Hypomagnesemia, renal AR 3 19
CLN3 Neuronal ceroid lipofuscinosis, type 3 AR 85 70
CLN5 Neuronal ceroid lipofuscinosis, type 5 AR 47 43
CLN6 Neuronal ceroid lipofuscinosis, type 6 AR 25 81
CLN8 Neuronal ceroid lipofuscinosis, type 8 AR 34 41
CNNM1 Hypomagnesemia AD/AR
CNNM2 Hypomagnesemia, renal AR 5 6
CNNM4 Jalili syndrome AR 10 23
COG1 Congenital disorder of glycosylation AR 2 2
COG4 Congenital disorder of glycosylation AR 8 4
COG5 Congenital disorder of glycosylation AR 3 10
COG6 Congenital disorder of glycosylation AR 5 7
COG7 Congenital disorder of glycosylation AR 4 5
COG8 Congenital disorder of glycosylation AR 4 7
COL2A1 Avascular necrosis of femoral head, Rhegmatogenous retinal detachment, Epiphyseal dysplasia, with myopia and deafness, Czech dysplasia, Achondrogenesis type 2, Platyspondylic dysplasia Torrance type, Hypochondrogenesis, Spondyloepiphyseal dysplasia congenital (SEDC), Spondyloepimetaphyseal dysplasia (SEMD) Strudwick type, Kniest dysplasia, Spondyloperipheral dysplasia, Mild SED with premature onset arthrosis, SED with metatarsal shortening, Stickler syndrome type 1 AD 138 541
COL11A2 Weissenbacher-Zweymuller syndrome, Deafness, Otospondylomegaepiphyseal dysplasia, Fibrochondrogenesis, Stickler syndrome type 3 (non-ocular) AD/AR 23 54
COQ2 Coenzyme Q10 deficiency AR 13 28
COQ6 Coenzyme Q10 deficiency AR 14 15
COQ9 Coenzyme Q10 deficiency AR 2 3
CPOX Coproporphyria, Harderoporphyria AD/AR 15 68
CPS1 Carbamoylphosphate synthetase I deficiency AR 19 261
CPT1A Carnitine palmitoyltransferase deficiency AR 49 46
CPT1B Carnitine palmitoyltransferase deficiency AD
CPT2 Carnitine palmitoyltransferase II deficiency AR 47 104
CTNS Cystinosis AR 49 142
CTSA Galactosialidosis AR 17 36
CTSC Periodontitis, juvenile, Haim-Munk syndrome, Papillon-Lefevre syndrome AR 16 91
CTSD Ceroid lipofuscinosis, neuronal AR 13 14
CTSK Pycnodysostosis AR 24 54
DBT Maple syrup urine disease AR 32 71
DDOST Congenital disorder of glycosylation AR 2 2
DGUOK Mitochondrial DNA depletion syndrome AR 19 60
DHCR7 Smith-Lemli-Opitz syndrome AR 64 214
DHDDS Retinitis pigmentosa AR 1 5
DLD Dihydrolipoyl dehydrogenase deficiency AR 24 21
DOLK Congenital disorder of glycosylation AR 7 10
DPAGT1 Congenital disorder of glycosylation, Myasthenic syndrome, congenital AR 15 30
DPM1 Congenital disorder of glycosylation AR 7 8
DPM2 Congenital disorder of glycosylation AR 2 2
DPM3 Congenital disorder of glycosylation AR 2 1
DPYD 5-fluorouracil toxicity AD/AR 52 88
DYM Dyggve-Melchior-Clausen dysplasia, Smith-McCort dysplasia AR 20 34
ECHS1 Mitochondrial short-chain enoyl-CoA hydratase 1 deficiency AR 17 30
EGF Hypomagnesemia, renal AR 1 2
ENO3 Glycogen storage disease AR 3 4
EPM2A Epilepsy, progressive myoclonic AR 15 74
ETFA Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 8 27
ETFB Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 6 14
ETFDH Glutaric aciduria, Multiple acyl-CoA dehydrogenase deficiency AR 37 169
FBP1 Fructose-1,6-bisphosphatase deficiency AR 18 41
FBXL4 Mitochondrial DNA depletion syndrome AR 54 36
FECH Protoporphyria, erythropoietic AD/AR 14 192
FH Hereditary leiomyomatosis and renal cell cancer AD/AR 142 174
FLNA Frontometaphyseal dysplasia, Osteodysplasty Melnick-Needles, Otopalatodigital syndrome type 1, Otopalatodigital syndrome type 2, Terminal osseous dysplasia with pigmentary defects XL 102 220
FLNB Larsen syndrome (dominant), Atelosteogenesis type 1, Atelosteogenesis type 3, Spondylo-carpal-tarsal dyspasia AD/AR 41 102
FOLR1 Cerebral folate deficiency AR 8 27
FUCA1 Fucosidosis AR 17 31
FXYD2 Hypomagnesemia, renal AD 1 1
G6PC Glycogen storage disease AR 33 112
GAA Glycogen storage disease AR 136 528
GALC Krabbe disease AR 66 233
GALNS Mucopolysaccharidosis (Morquio syndrome) AR 41 333
GAMT Guanidinoacetate methyltransferase deficiency AR 16 55
GATM Arginine:glycine amidinotransferase deficiency AR 6 16
GBA* Gaucher disease AR 76 459
GBE1 Glycogen storage disease AR 30 71
GCDH Glutaric aciduria AR 64 205
GCH1 Dopa-Responsive Dystonia Hyperphenylalaninemia, BH4-deficient, GTP Cyclohydrolase 1-Deficient Dopa-Responsive Dystonia AD/AR 28 234
GCK Hyperinsulinemic hypoglycemia, familial, Diabetes mellitus, permanent neonatal AD/AR 157 795
GIF Intrinsic factor deficiency AR 7 20
GLA Fabry disease XL 188 910
GLB1 GM1-gangliosidosis, Mucopolysaccharidosis (Morquio syndrome) AR 60 212
GLDC Glycine encephalopathy AR 95 423
GLUD1* Hyperammonemia-hyperinsulinism, Hyperinsulinemic hypoglycemia AD/AR 13 38
GMPPA Alacrima, achalasia, and mental retardation syndrome AR 5 11
GNE Inclusion body myopathy, Nonaka myopathy, Sialuria AD/AR 50 200
GNPAT Rhizomelic chondrodysplasia punctata, rhizomelic AR 8 14
GNPTAB Mucolipidosis AR 151 175
GNPTG Mucolipidosis AR 26 42
GNS Mucopolysaccharidosis (Sanfilippo syndrome) AR 6 25
GPC3 Simpson-Golabi-Behmel syndrome XL 26 72
GPHN Hyperekplexia, Molybdenum cofactor deficiency AD/AR 25 20
GUSB* Mucopolysaccharidosis AR 24 61
GYG1 Glycogen storage disease AR 8 11
GYS1 Glycogen storage disease AR 5 5
GYS2 Glycogen storage disease AR 14 22
HADH 3-hydroxyacyl-CoA dehydrogenase deficiency AR 10 26
HADHA Trifunctional protein deficiency, Long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency AR 42 68
HADHB Trifunctional protein deficiency AR 17 57
HAMP Hemochromatosis AR 5 14
HCFC1 Combined methylmalonic acidemia and hyperhomocysteinemia XL 8 16
HEXA Tay-Sachs disease, GM2-gangliosidosis, Hexosaminidase A deficiency AR 108 183
HEXB Sandhoff disease AR 33 111
HFE Hemochromatosis AR/Digenic 9 53
HFE2 Hemochromatosis AR 15 50
HGSNAT Mucopolysaccharidosis (Sanfilippo syndrome), Retinitis pigmentosa AR 24 68
HLCS Holocarboxylase synthetase deficiency AR 21 47
HMBS Porphyria, acute intermittent, Hydroxymethylbilane synthase deficiency AD/AR 51 415
HMGCL 3-hydroxy-3-methylglutaryl-CoA lyase deficiency AR 9 58
HMGCS2 3-hydroxy-3-methylglutaryl-CoA synthase 2 deficiency AR 8 27
HNF1A Maturity onset diabetes of the young, Renal cell carcinoma, nonpapillary clear cell, Liver adenomatosis AD 61 511
HNF1B Renal cell carcinoma, nonpapillary chromophobe, Renal cysts and diabetes syndrome AD 32 225
HNF4A Congenital hyperinsulinism, diazoxide-responsive, Maturity onset diabetes of the young, Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young AD 24 145
HPD Hawksinuria, Tyrosinemia AD/AR 4 9
HRAS Costello syndrome, Congenital myopathy with excess of muscle spindles AD 39 27
HSD17B4 Perrault syndrome AR 41 96
HSD17B10 17-beta-hydroxysteroid dehydrogenase X deficiency, Mental retardation, syndromic XL 9 12
HYAL1 Mucopolysaccharidosis AR 2 3
IDS* Mucopolysaccharidosis XL 73 627
IDUA Mucopolysaccharidosis AR 49 252
IFIH1 Singleton-Merten syndrome AD 13 15
INSR Hyperinsulinemic hypoglycemia, familial, Rabson-Mendenhall syndrome, Donohoe syndrome AD/AR 40 175
ISCU Myopathy with lactic acidosis AR 3 2
IVD Isovaleric acidemia AR 33 81
KCNA1 Episodic ataxia/myokymia syndrome AD 22 40
KCNJ2 Short QT syndrome, Andersen syndrome, Long QT syndrome, Atrial fibrillation AD 38 86
KCNJ11 Hyperinsulinemic hypoglycemia, Diabetes, permanent neonatal, Diabetes mellitus, transient neonatal AD/AR 52 170
L2HGDH L-2-hydroxyglutaric aciduria AR 11 75
LAMA2 Muscular dystrophy, congenital merosin-deficient AR 90 256
LAMP2 Danon disease XL 54 94
LDB3 Dilated cardiomyopathy (DCM), Myopathy, myofibrillar AD 9 12
LDHA Glycogen storage disease AR 1 8
LIPA Wolman disease, Cholesterol ester storage disease AR 12 78
LMBRD1 Methylmalonic aciduria and homocystinuria AR 3 9
LMNA Heart-hand syndrome, Slovenian, Limb-girdle muscular dystrophy, Muscular dystrophy, congenital, LMNA-related, Lipodystrophy (Dunnigan), Emery-Dreiffus muscular dystrophy, Malouf syndrome, Dilated cardiomyopathy (DCM), Mandibuloacral dysplasia type A, Progeria Hutchinson-Gilford type AD/AR 211 513
LPIN1 Myoglobinuria, acute, recurrent AR 6 29
MAGT1 Immunodeficiency, with magnesium defect, Epstein-Barr virus infection and neoplasia XL 5 14
MAN1B1 Mental retardation AR 6 21
MANBA Mannosidosis, lysosomal AR 12 18
MCCC1 3-Methylcrotonyl-CoA carboxylase 1 deficiency AR 25 103
MCCC2 3-Methylcrotonyl-CoA carboxylase 2 deficiency AR 19 113
MCEE Methylmalonyl-CoA epimerase deficiency AR 2 4
MCOLN1 Mucolipidosis AR 45 35
MFN2 Hereditary motor and sensory neuropathy, Charcot-Marie-Tooth disease AD/AR 52 218
MFSD8 Ceroid lipofuscinosis, neuronal AR 19 43
MGAT2 Congenital disorder of glycosylation AR 5 5
MMAA Methylmalonic acidemia AR 41 53
MMAB Methylmalonic acidemia AR 22 39
MMACHC Methylmalonic aciduria and homocystinuria AR 26 91
MMADHC Methylmalonic aciduria and homocystinuria AR 15 13
MMGT1 Hypomagnesemia XL
MOCS1 Molybdenum cofactor deficiency AR 7 32
MOCS2 Molybdenum cofactor deficiency AR 9 12
MOGS Congenital disorder of glycosylation AR 6 5
MPDU1 Congenital disorder of glycosylation AR 4 5
MPI Congenital disorder of glycosylation AR 17 18
MPV17 Mitochondrial DNA depletion syndrome AR 31 41
MTHFR Homocystinuria due to MTHFR deficiency AR 57 119
MTR Methylmalonic acidemia AR 12 40
MTRR Homocystinuria-megaloblastic anemia, cobalamin E AR 8 30
MUT Methylmalonic acidemia due to methylmalonyl-CoA mutase deficiency AR 101 339
MYOT Myopathy, myofibrillar AD 8 16
NAGLU Mucopolysaccharidosis (Sanfilippo syndrome) AR 28 166
NAGS N-acetylglutamate synthase deficiency AR 11 45
NDUFS1 Mitochondrial complex I deficiency AR 22 25
NEU1 Sialidosis AR 22 59
NHLRC1 Epilepsy, progressive myoclonic AR 14 70
NIPA2 Hypomagnesemia AD/AR 4
NPC1 Niemann-Pick disease AR 107 447
NPC2 Niemann-pick disease AR 16 27
OAT Gyrate atrophy of choroid and retina AR 63 70
OPA1 Optic atrophy AD/AR 80 372
OPA3 Optic atrophy, 3-methylglutaconic aciduria AD/AR 8 15
OTC Ornithine transcarbamylase deficiency XL 331 502
OXCT1 Succinyl CoA:3-oxoacid CoA transferase deficiency AR 7 24
PAH Hyperphenylalaninemia, non-PKU mild, Phenylketonuria AR 217 910
PC Pyruvate carboxylase deficiency AR 29 39
PCBD1 Hyperphenylalaninemia, BH4-deficient AR 6 11
PCCA Propionic acidemia AR 43 120
PCCB Propionic acidemia AR 40 111
PCK1 Phosphoenolpyruvate carboxykinase 1 deficiency AD/AR 2 3
PCK2 Phosphoenolpyruvate carboxykinase 2 deficiency AD/AR 2
PDHA1 Leigh syndrome, Pyruvate dehydrogenase E1-alpha deficiency XL 51 170
PDHB Pyruvate dehydrogensae E1-beta deficiency AR 4 13
PDHX Pyruvate dehydrogenase E3-binding protein deficiency AR 14 22
PDSS1 Coenzyme Q10 deficiency AR 5 3
PDSS2 Coenzyme Q10 deficiency AR 7 3
PDX1 Pancreatic agenesis, Neonatal diabetes mellitus AD/AR 10 26
PEX1 Heimler syndrome AR 77 130
PEX2 Zellweger syndrome, Peroxisome biogenesis disorder AR 9 18
PEX3 Zellweger syndrome, Peroxisome biogenesis disorder AR 5 9
PEX5 Adrenoleukodystrophy, neonatal, Rhizomelic chondrodysplasia punctata, Zellweger syndrome, Peroxisome biogenesis disorder AR 7 14
PEX6 Heimler syndrome AR 25 105
PEX7 Refsum disease, Rhizomelic CDP type 1 AR 36 52
PEX10 Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorder, Ataxia AR 18 29
PEX11B Zellweger syndrome, Peroxisome biogenesis disorder AR 3 6
PEX12 Zellweger syndrome, Peroxisome biogenesis disorder AR 19 37
PEX13 Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorder AR 5 10
PEX16 Zellweger syndrome, Peroxisome biogenesis disorder AR 8 12
PEX26 Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorder AR 11 24
PFKM Glycogen storage disease AR 11 26
PGAM2 Glycogen storage disease AR 3 9
PGK1 Phosphoglycerate kinase 1 deficiency XL 15 26
PGM1 Congenital disorder of glycosylation AR 9 30
PHKA1 Glycogen storage disease XL 6 8
PHKA2 Glycogen storage disease XL 22 113
PHKB Glycogen storage disease AR 8 24
PHKG1* Glycogen storage disease due to muscle phosphorylase kinase deficiency AD/AR
PHKG2 Glycogen storage disease AR 7 31
PHYH Refsum disease AR 10 36
PLIN1 Lipodystrophy, familial partial AD 3 5
PMM2 Congenital disorder of glycosylation AR 58 123
POLG POLG-related ataxia neuropathy spectrum disorders, Sensory ataxia, dysarthria, and ophthalmoparesis, Alpers syndrome, Progressive external ophthalmoplegia with mitochondrial DNA deletions, Mitochondrial DNA depletion syndrome AD/AR 92 274
POLG2 Progressive external ophthalmoplegia with mitochondrial DNA deletions AD 5 13
PPARG Insulin resistance, Lipodystrophy, familial, partial AD/Digenic (Severe digenic insulin resistance can be due to digenic mutations in PPP1R3A and PPARG) 19 47
PPOX Porphyria variegata AD/AR 15 179
PPT1 Ceroid lipofuscinosis, neuronal AR 84 77
PRKAG2 Hypertrophic cardiomyopathy (HCM), Wolff-Parkinson-White syndrome AD 19 53
PRKAG3 Increased glyogen content in skeletal muscle AD 1 1
PRODH* Hyperprolinemia AR 41 10
PSAP Krabbe disease, atypical, Metachromatic leukodystrophy due to saposin-b deficiency, Combined saposin deficiency, Gaucher disease, atypical, due to saposin C deficiency AR 16 24
PTRF Lipodystrophy, congenital generalized AR 8 15
PTS Hyperphenylalaninemia, BH4-deficient AR 16 90
PYGL Glycogen storage disease AR 20 43
PYGM Glycogen storage disease AR 62 153
QDPR Hyperphenylalaninemia, BH4-deficient AR 9 61
RAI1 Smith-Magenis syndrome AD 26 108
RBCK1 Polyglucosan body myopathy AR 8 14
RFT1 Congenital disorder of glycosylation AR 9 8
RNASEH2A Aicardi-Goutières syndrome AR 13 21
RNASEH2B Aicardi-Goutières syndrome AR 10 40
RNASEH2C Aicardi-Goutières syndrome AR 6 14
RPN2 Congenital disorder of glycosylation AD/AR 1
RRM2B Progressive external ophthalmoplegia with mitochondrial DNA deletions, Mitochondrial DNA depletion syndrome AD/AR 41 40
RYR1 Central core disease, Malignant hyperthermia, Minicore myopathy with external ophthalmoplegia, Centronuclear myopathy, Minicore myopathy, Multicore myopathy AD/AR 162 607
SAMHD1 Aicardi-Goutières syndrome AR 22 51
SCN4A Hyperkalemic periodic paralysis, Myotonia, potassium-aggravated, Paramyotonia congenita, Myasthenic syndrome, congenital, Normokalemic potassium-sensitive periodic paralysis AD/AR 57 110
SEC23B Anemia, dyserythropoietic congenital AR 14 111
SGSH Mucopolysaccharidosis (Sanfilippo syndrome) AR 29 145
SLC2A2 Glycogen storage disease, Fanconi-Bickel syndrome, Neonatal diabetes mellitus AR 17 71
SLC3A1 Cystinuria AR 17 177
SLC6A8* Creatine deficiency syndrome XL 25 124
SLC6A19 AR 5 23
SLC7A7 Lysinuric protein intolerance AR 52 66
SLC7A9 Cystinuria AD/AR 18 124
SLC12A3 Gitelman syndrome AR 33 481
SLC16A1 Hyperinsulinemic hypoglycemia, familial, Erythrocyte lactate transporter defect, Monocarboxylate transporter 1 deficiency AD/AR 11 14
SLC17A5 Sialuria, Finnish (Salla disease), Infantile sialic acid storage disorder AR 42 35
SLC22A5 Carnitine deficiency, systemic primary AR 76 117
SLC25A3 Micochondrial phosphate carrier deficiency AR 2 5
SLC25A4 Progressive external ophthalmoplegia with mitochondrial DNA deletions, Mitochondrial DNA depletion syndrome AD/AR 12 13
SLC25A13 Citrin deficiency AR 23 109
SLC25A15* Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome AR 21 36
SLC25A20 Carnitine-acylcarnitine translocase deficiency AR 11 41
SLC30A10 Hypermanganesemia with dystonia, polycythemia, and cirrhosis AR 15 14
SLC35A1 Congenital disorder of glycosylation AR 1 2
SLC35A2 Congenital disorder of glycosylation XL 13 15
SLC35C1 Congenital disorder of glycosylation, Leukocyte adhesion deficiency AR 4 7
SLC37A4 Glycogen storage disease AR 27 108
SLC39A4 Acrodermatitis enteropathica AR 13 50
SLC40A1 Hemochromatosis AD 13 56
SLC41A2 Hypomagnesemia AD/AR
SLC41A3 Hypomagnesemia AD/AR
SLC46A1 Folate malabsorption AR 17 20
SMPD1 Niemann-Pick disease AR 81 238
SPG7 Spastic paraplegia AR 53 104
SRD5A3* Kahrizi syndrome, Congenital disorder of glycosylation AR 12 16
SSR4 Congenital disorder of glycosylation XL 5 6
STT3A Congenital disorder of glycosylation AR 1 1
STT3B Congenital disorder of glycosylation AR 1 2
SUCLA2 Mitochondrial DNA depletion syndrome AR 8 27
SUCLG1 Mitochondrial DNA depletion syndrome AR 11 28
SUMF1 Multiple sulfatase deficiency AR 21 52
SUOX Sulfocysteinuria AR 6 28
TAZ 3-Methylglutaconic aciduria, (Barth syndrome) XL 39 151
TBC1D4 Diabetes mellitus, noninsulin-dependent AR 1 2
TCF4 Corneal dystrophy, Fuchs endothelial, Pitt-Hopkins syndrome AD 67 136
TCN2 Transcobalamin II deficiency AR 8 33
TFR2 Hemochromatosis AR 16 50
TIMM8A* Mohr-Tranebjaerg syndrome, Jensen syndrome, Opticoacoustic nerve atrophy with dementia XL 10 21
TK2 Mitochondrial DNA depletion syndrome AR 38 45
TMEM70 Mitochondrial complex V (ATP synthase) deficiency AR 10 18
TMEM126A Optic atrophy AR 2 1
TMEM165 Congenital disorder of glycosylation AR 4 6
TPP1 Spinocerebellar ataxia, Neuronal ceroid lipofuscinosis type 2 AR 52 110
TREX1 Vasculopathy, retinal, with cerebral leukodystrophy, Chilblain lupus, Aicardi-Goutières syndrome AD/AR 27 66
TRPM6 Hypomagnesemia, intestinal AR 15 58
TRPM7 Amyotrophic lateral sclerosis-parkinsonism-dementia complex AD/AR 2
TUSC3 Mental retardation AR 3 14
TYMP Mitochondrial DNA depletion syndrome AR 85 94
UCP2 Hyperinsulinism AD/AR 7
UROD Porphyria cutanea tarda, Porphyria, hepatoerythropoietic AD/AR 15 122
UROS Porphyria, congenital erythropoietic AR 22 49
WFS1 Wolfram syndrome, Deafness AD/AR 65 343
ZMPSTE24 Restrictive dermopathy, lethal, Mandibuloacral dysplasia with B lipodystrophy AD/AR 13 33

*Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/). The list of associated (gene specific) phenotypes are generated from CDG (http://research.nhgri.nih.gov/CGD/) or Orphanet (http://www.orpha.net/) databases.

Gene Genomic location HG19 HGVS RefSeq RS-number
ACADM Chr1:76211473 c.600-18G>A NM_000016.4 rs370523609
ALAS2 ChrX:55057617 c.-258C>G NM_000032.4 rs140772352
AMT Chr3:49459938 c.-55C>T NM_000481.3 rs386833677
ASS1 Chr9:133355236 c.773+49C>T NM_000050.4 rs763389916
COG6 Chr13:40273614 c.1167-24A>G NM_020751.2 rs730882236
DBT Chr1:100672742 c.1018-550A>G NM_001918.3 rs796052135
GAA Chr17:78078341 c.-32-13T>G NM_000152.3 rs386834236
GAA Chr17:78078351 c.-32-3C>A NM_000152.3
GAA Chr17:78082266 c.1076-22T>G NM_000152.3 rs762260678
GBE1 Chr3:81542963 c.2053-3358_2053-3350delGTGTGGTGGinsTGTTTTTTACATGACAGGT NM_000158.3
GLA ChrX:100654735 c.640-801G>A NM_000169.2 rs199473684
GNPTG Chr16:1412562 c.610-16_609+28del NM_032520.4 rs193302853
HADH Chr4:108945190 c.636+471G>T NM_001184705.2 rs786200932
HCFC1 ChrX:153237261 c.-970T>C NM_005334.2 rs398122908
ISCU Chr12:108961426 c.418+382G>C NM_213595.2 rs767000507
KCNJ11 Chr11:17409772 c.-134G>T NM_000525.3 rs387906398
LMNA Chr1:156100609 c.513+45T>G NM_170707.3
MOCS1 Chr6:39874534 c.*365_*366delAG NM_005943.5 rs397518419
MTHFR Chr1:11863212 c.-13-28_-13-27delCT NM_005957.4 rs786204005
MTHFR Chr1:11850973 c.1753-18G>A NM_005957.4 rs777661576
MUT Chr6:49427219 c.-39-1G>A NM_000255.3
PAH Chr12:103237407 c.1199+17G>A NM_000277.1 rs62508613
PAH Chr12:103271835 c.353-507G>T NM_000277.1 rs863225301
PDHA1 ChrX:19377861 c.*79_*90dupAGTCAATGAAAT NM_001173454.1
PEX7 Chr6:137143759 c.-45C>T NM_000288.3 rs267608252
PPT1 Chr1:40539203 c.*526_*529delATCA NM_000310.3 rs386833624
PTS Chr11:112098994 c.84-323A>T NM_000317.2 rs794726657
PYGM Chr11:64525847 c.425-26A>G NM_005609.2 rs764313717
RYR1 Chr19:39074134 c.14647-1449A>G NM_000540.2 rs193922886
SLC16A1 Chr1:113498814 c.-202G>A NM_003051.3 rs387906403
SLC16A1 Chr1:113499002 c.-391_-390insACGCCGGTCACGTGGCGGGGTGGGG NM_003051.3 rs606231172
STT3B Chr3:31663820 c.1539+20G>T NM_178862.1
TCN2 Chr22:31011112 c.581-176A>G NM_000355.3 rs372866837
TIMM8A ChrX:100601671 c.133-23A>C NM_004085.3 rs869320666
TMEM165 Chr4:56284334 c.792+182G>A NM_018475.4 rs793888506
UROS Chr10:127511774 c.-203T>C NM_000375.2 rs869320670
UROS Chr10:127511794 c.-223C>A NM_000375.2 rs869320669
UROS Chr10:127505271 c.-26-177T>C NM_000375.2 rs397515348
UROS Chr10:127505277 c.-26-183G>A NM_000375.2 rs397515349
UROS Chr10:127505287 c.-26-193C>A NM_000375.2 rs397515350
UROS Chr10:127505291 c.-26-197C>A NM_000375.2 rs397515351

The strengths of this test include:

  • Blueprint Genetics is one of the few laboratories worldwide with CAP and ISO-15189 accreditation for NGS panels and CLIA certification
  • Superior sequencing quality
  • Careful selection of genes based on current literature, our experience and the most current mutation databases
  • Transparent and easy access to quality and performance data at the patient level that are accessible via our Nucleus portal
  • Transparent and reproducible analytical validation for each panel (see Test performance section; for complete details, see our Analytic Validation)
  • Sequencing and high resolution del/dup analysis available in one test
  • Inclusion of non-coding disease causing variants where clinically indicated (please see individual Panel descriptions)
  • Interpretation of variants following ACMG variant classification guidelines
  • Comprehensive clinical statement co-written by a PhD geneticist and a clinician specialist

 

This test does not detect the following:

  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Variants in regulatory or non-coding regions of the gene unless otherwise indicated (please see Non-coding disease causing variants covered by the panel). This mean for instance intronic variants locating deeper than 15 nucleotides from the exon-intron boundary.

 

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments
  • Disorders caused by long repetitive sequences (e.g. trinucleotide repeat expansions)

 

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

Blueprint Genetics offers a Comprehensive Metabolism Panel that covers classical genes associated with Aicardi-Goutières syndrome, familial hyperinsulinism, inborn error of metabolism, magnesium deficiency, metabolic myopathies, mitochondrial DNA depletion syndrome, periodic paralysis, primary CoQ10 deficiency, rhabdomyolysis, rhizomelic chondrodysplasia punctata and zellweger Syndrome Spectrum. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Average sensitivity and specificity in Blueprint NGS Panels is 99.3% and 99.9% for detecting SNPs. Sensitivity to for indels vary depending on the size of the alteration: 1-10bps (96.0%), 11-20 bps (88.4%) and 21-30 bps (66.7%). The longest detected indel was 46 bps by sequence analysis. Detection limit for Del/Dup (CNV) analysis varies through the genome depending on exon size, sequencing coverage and sequence content. The sensitivity is 71.5% for single exon deletions and duplications and 99% for three exons’ deletions and duplications. We have validated the assays for different starting materials including EDTA-blood, isolated DNA (no FFPE) and saliva that all provide high-quality results. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile.

The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (http://www.1000genomes.org), the NHLBI GO Exome Sequencing Project (ESP; http://evs.gs.washington.edu/EVS), the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org), ClinVar database of genotype-phenotype associations (http://www.ncbi.nlm.nih.gov/clinvar) and the Human Gene Mutation Database (http://www.hgmd.cf.ac.uk). The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (http://sift.jcvi.org), Polyphen (http://genetics.bwh.harvard.edu/pph2/), and Mutation Taster (http://www.mutationtaster.org).

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes

SEQ 81479
DEL/DUP 81479


ICD codes

Commonly used ICD-10 codes when ordering the Comprehensive Metabolism Panel

ICD-10 Disease
Z13.228 Inborn error of metabolism

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

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