Comprehensive Skeletal / Malformation Syndrome Panel

SEQmethod-seq-icon Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 21 days. DEL/DUPmethod-dup-icon Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 21 days. PLUSmethod-plus-icon Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 21 days.

Test code: MA3201

The Blueprint Genetics Comprehensive Skeletal / Malformation Syndrome Panel is a 429 gene test for genetic diagnostics of patients with clinical suspicion of malformations or skeletal syndromes.

Blueprint Genetics (BpG) offers comprehensive genetic diagnostics for malformations. In total the malformation category consists of 32 unique panels including 429 unique genes, all covered by this comprehensive panel. Inherited skeletal diseases are known to be difficult to subtype and divide to categories. This panel covers vast majority of the genes listed in the Nosology 2015 (PMID: 26394607) and all genes in the category (Malformations) therefore providing maximal differential diagnostic power in the field.

About Malformation Syndromes

This panel covers broad spectrum of connective tissue and skeletal disorders leading to syndromes manifesting from isolated defects, growth abnormalities to malformations in the whole body level. Some of the panels cover organ specific malformations such as Hirschsprung disease and gastrointestinal atresias, cerebral cavernous malformations and neurofibromatosis. Genetic diagnostics in these diseases is the most efficient way to subtype the diseases and enable individualized treatment and management decisions. Moreover, detection of causative mutation establishes inheritance mode of the disease in the family which is essential for informed genetic counseling.


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.

Genes in the Comprehensive Skeletal / Malformation Syndrome Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
ABCC6*Pseudoxanthoma elasticumAR39285
ACP5Spondyloenchondrodysplasia with immune dysregulationAR1024
ACTB*Baraitser-Winter syndromeAD2726
ACTG1*Deafness, Baraitser-Winter syndromeAD1737
ACVR1Fibrodysplasia ossificans progressivaAD1218
ADAMTS2Ehlers-Danlos syndromeAR311
ADAMTS10Weill-Marchesani syndromeAR813
ADAMTSL2Geleophysic dysplasiaAR726
ADGRG1Polymicrogyria, bilateral frontoparietal, Polymicrogyris, bilateral perisylvianAR22
AGPSRhizomelic chondrodysplasia punctata type 3AR48
AGRNMyasthenic syndrome, congenitalAR1010
AKT1Proteus syndrome, Cowden syndromeAD39
AKT3Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndromeAD821
ALPLOdontohypophosphatasia, Hypophosphatasia perinatal lethal, infantile, juvenile and adult formsAD/AR32270
ALX3Frontonasal dysplasia type 1AR77
ALX4Frontonasal dysplasia type 2, Parietal foraminaAD/AR1322
AMER1Osteopathia striata with cranial sclerosisXL934
ANKHCalcium pyrophosphate deposition disease (familial chondrocalcinosis type 2), Craniometaphyseal dysplasia autosomal dominant typeAD1221
ANO5Gnathodiaphyseal dysplasia, LGMD2L and distal MMD3 muscular dystrophiesAR42106
ARFGEF2Heterotopia, periventricularAR511
ARHGAP31Adams-Oliver syndromeAD24
ARID1ACoffin-Siris syndrome, Mental retardationAD1112
ARID1BCoffin-Siris syndrome, Mental retardationAD53126
ARSE*Chondrodysplasia punctata X-linked recessive, brachytelephalangic type (CDPX1)XL1646
ARXLissencephaly, Epileptic encephalopathy, Corpus callosum, agenesis of, with abnormal genitalia, Partington syndrome, Proud syndrome, Hydranencephaly with abnormal genitalia, Mental retardationXL5680
ASPAAspartoacylase deficiency (Canavan disease)AR1990
ASXL1Bohring-Opitz syndromeAD1427
ATP6V0A2Cutis laxa, Wrinkly skin syndromeAR1652
ATRCutaneous telangiectasia and cancer syndrome, Seckel syndromeAD/AR613
B3GALNT2Muscular dystrophy-dystroglycanopathyAR713
B3GALT6Spondyloepimetaphyseal dysplasia with joint laxity, Ehlers-Danlos syndromeAR1422
B4GALT7Ehlers-Danlos syndrome, progeroid formAR88
BHLHA9Syndactyly Malik-Percin type, mesoaxial synostotic, with phalangeal reduction, Split hand-foot malformation with long bone deficiency (SHFLD3), Gollop-WolfgangAR429
BIN1Myopathy, centronuclearAR615
BMP1Osteogenesis imperfectaAR611
BMP2Brachydactyly type A2AD126
BMP4Microphthalmia, syndromic, Orofacial cleftAD942
BMPR1A*Polyposis, juvenile intestinalAD38108
BMPR1BAcromesomelic dysplasia, Demirhan, Brachydactyly C/Symphalangism-like pheno, Brachydactyly type A2AD/AR1113
BRWD3Mental retardationXL69
CA2Osteopetrosis, with renal tubular acidosisAR830
CANT1Desbuquois dysplasiaAR1725
CAPN3Muscular dystrophy, limb-girdle, Eosinophilic myositisAR102400
CASKMental retardation and microcephaly with pontine and cerebellar hypoplasia, FG syndrome, Mental retardationXL4380
CASRHypocalcemia, Neonatal hyperparathyroidism, Familial Hypocalciuric hypercalcemia with transient Neonatal hyperparathyroidismAD/AR78392
CBSHomocystinuria due to cystathionine beta-synthase deficiencyAR51192
CCM2Cerebral cavernous malformationsAD1479
CCND2Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndromeAD710
CDC6Meier-Gorlin syndrome (Ear-patella-short stature syndrome)AR13
CDKN1CBeckwith-Wiedemann syndrome, IMAGE syndromeAD2579
CDT1Meier-Gorlin syndrome (Ear-patella-short stature syndrome)AR68
CENPFCiliary dyskinesia -Lethal CiliopathyAR86
CENPJSeckel syndrome, MicrocephalyAR236
CEP63Seckel syndromeAR42
CEP152Seckel syndrome, MicrocephalyAR1317
CFL2Nemaline myopathyAR23
CHATMyasthenic syndrome, congenitalAR1468
CHD7Isolated gonadotropin-releasing hormone deficiency, CHARGE syndromeAD128746
CHKBMuscular dystrophy, congenital, megaconialAR522
CHRNA1Myasthenic syndrome, congenitalAD/AR1932
CHRNB1Myasthenic syndromeAD/AR58
CHRNDMyasthenic syndromeAD/AR1219
CHRNEMyasthenic syndromeAD/AR26121
CHRNGMultiple pterygium syndrome, Escobar syndromeAR1129
CHST3Spondyloepiphyseal dysplasia with congenital joint dislocations (recessive Larsen syndrome)AR1335
CHST14Ehlers-Danlos syndrome, musculocontracturalAR1021
CLCN5Proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis, Hypophosphatemic rickets,, Nephrolithiasis, I, Dent diseaseXL37255
COL1A1Ehlers-Danlos syndrome, Caffey disease, Osteogenesis imperfecta type 1, Osteogenesis imperfecta type 2, Osteogenesis imperfecta type 3, Osteogenesis imperfecta type 4AD120883
COL1A2Ehlers-Danlos syndrome, cardiac valvular form, Osteogenesis imperfecta type 1, Osteogenesis imperfecta type 2, Osteogenesis imperfecta type 3, Osteogenesis imperfecta type 4AD79473
COL2A1Avascular 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 1AD106537
COL3A1Ehlers-Danlos syndromeAD452617
COL4A1Schizencephaly, Anterior segment dysgenesis with cerebral involvement, Retinal artery tortuosity, Porencephaly, Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps, Brain small vessel diseaseAD2788
COL4A2Hemorrhage, intracerebralAD512
COL4A4Alport syndromeAD/AR17170
COL5A1Ehlers-Danlos syndromeAD43133
COL5A2Ehlers-Danlos syndromeAD1223
COL6A1Bethlem myopathy, Ullrich congenital muscular dystrophyAD/AR4695
COL6A2Epilepsy, progressive myoclonic, Bethlem myopathy, Myosclerosis, congenital, Ullrich congenital muscular dystrophyAD/AR65134
COL6A3Bethlem myopathy, Dystonia, Ullrich congenital muscular dystrophyAD/AR36105
COL9A1Stickler syndrome recessive type, Multiple epiphyseal dysplasia type 6 (EDM6)AR34
COL9A2Stickler syndrome, Multiple epiphyseal dysplasia type 2 (EDM2)AR512
COL9A3Multiple epihyseal dysplasia type 3 (EDM3)AD316
COL10A1Metaphyseal chondrodysplasia, SchmidAD2050
COL11A1Marshall syndrome, Fibrochondrogenesis, Stickler syndrome type 2AD/AR1876
COL11A2Weissenbacher-Zweymuller syndrome, Deafness, Otospondylomegaepiphyseal dysplasia, Fibrochondrogenesis, Stickler syndrome type 3 (non-ocular)AD/AR1751
COLQMyasthenic syndrome, congenitalAR1266
COMPPseudoachondroplasia, Multiple ephiphyseal dysplasiaAD33182
CREBBPRubinstein-Taybi syndromeAD103332
CRTAPOsteogenesis imperfecta type 2, Osteogenesis imperfecta type 3, Osteogenesis imperfecta type 4AR1124
CSPP1Jeune Asphyxiating Thoracic Dystrophy, Joubert syndromeAR2223
CUL4BMental retardation, syndromic, CabezasXL934
CUL73-M syndrome, Yakut short stature syndromeAR1868
CYP27B1Vitamin D-dependent ricketsAR2075
DCXLissencephaly, Subcortical laminal heterotopiaXL117138
DHCR7Smith-Lemli-Opitz syndromeAR42194
DIS3L2*Perlman syndromeAR69
DLL3Spondylocostal dysostosisAR921
DLL4Adams-Oliver syndromeAD910
DLX3Amelogenesis imperfecta, Trichodontoosseous syndromeAD26
DNM2Myopathy, Lethal akinesia and musculoskeletal abnormalities, with brain and retinal hemorrhages, Charcot-Marie-Tooth diseaseAD/AR2344
DNMT3ATatton-Brown-Rahman syndromeAD1118
DOCK6Adams-Oliver syndromeAR1319
DOK7Myasthenic syndrome, congenitalAR1568
DPAGT1Congenital disorder of glycosylation, Myasthenic syndrome, congenitalAR1228
DVL1Robinow syndromeAD913
DYMDyggve-Melchior-Clausen dysplasia, Smith-McCort dysplasiaAR2028
DYNC1H1Spinal muscular atrophy, Charcot-Marie-Tooth disease, Mental retardationAD3453
DYNC2H1Short -rib thoracic dysplasia with or without polydactyly type 1, Short -rib thoracic dysplasia with or without polydactyly type 3, Asphyxiating thoracic dysplasia (ATD; Jeune), SRPS type 2 (Majewski)AR/Digenic3498
DYRK1AMental retardationAD4050
EBPChondrodysplasia punctata, Male EBP disorder with neurologic defects (MEND)XL4389
EDN3Hirschsprung disease, Central hypoventilation syndrome, congenital, Waardenburg syndromeAD/AR621
EDNRBHirschsprung disease, ABCD syndrome, Waardenburg syndromeAD/AR562
EFEMP2Cutis laxaAR1115
EFNB1Craniofrontonasal dysplasiaXL15115
EFTUD2Mandibulofacial dysostosis with microcephaly, Esophageal atresia, syndromicAD1688
EGR2Neuropathy, Dejerine-Sottas disease, Charcot-Marie-Tooth diseaseAD/AR1223
EIF2AK3SED, Wolcott-Rallison typeAR771
EIF2B5Leukoencephalopathy with vanishing white matter, OvarioleukodystrophyAR1495
ELNCutis laxa, Supravalvular aortic stenosisAD67104
EMDEmery-Dreifuss muscular dystrophyXL28111
ENAMAmelogenesis imperfectaAR318
ENPP1Arterial calcification, Hypophosphatemic ricketsAR1772
EOGTAdams-Oliver syndromeAR33
EP300Rubinstein-Taybi syndromeAD2143
ERCC5Xeroderma pigmentosum, Xeroderma pigmentosum/Cockayne syndromeAR1751
ERCC6Xeroderma Pigmentosum-Cockayne Syndrome, De Sanctis-Cacchione syndromeAD/AR3791
ERCC8UV-sensitive syndrome, Cockayne syndromeAR939
ESCO2SC phocomelia syndrome, Roberts syndromeAR2930
EVCWeyers acrofacial dysostosis, Ellis-van Creveld syndromeAD/AR777
EVC2Ellis-van Creveld syndrome, Weyers acrodental dysostosisAD/AR2366
EXOSC3Pontocerebellar hypoplasiaAR918
EXT1Multiple cartilagenious exostoses 1AD28479
EXT2Multiple cartilagenious exostoses 2AD20230
EYA1Otofaciocervical syndrome, Branchiootic syndrome, Branchiootorenal syndromeAD33186
EZH2Weaver syndromeAD1436
FAM20AAmelogenesis imperfecta (Enamel-renal syndrome)AR940
FAM20CHypophosphatemia, hyperphosphaturia, dental anomalies, intracerebral calcifications and osteosclerosis (Raine syndrome)AR1322
FAM83HAmelogenesis imperfectaAD1327
FANCBFanconi anemiaXL714
FANCCFanconi anemiaAR3434
FBLN5Cutis laxa, Macular degeneration, age-relatedAD/AR1321
FBN1MASS syndrome, Shprintzen-Goldberg syndrome, Marfan syndrome, Acromicric dysplasia, Geleophysic dysplasia, Weill-Marchesani syndromeAD5192056
FBN2Congenital contractural arachnodactyly (Beals syndrome)AD3085
FGD1Aarskog-Scott syndrome, Mental retardation, syndromicXL1842
FGF3Deafness, congenital with inner ear agenesis, microtia, and microdontiaAR1220
FGF8Hypogonadotropic hypogonadismAD/Digenic1028
FGF23Tumoral calcinosis, hyperphosphatemic, Hypophosphatemic ricketsAD/AR716
FGFR1Pfeiffer syndrome, Trigonocephaly, Hypogonadotropic hypogonadism, Osteoglophonic Dwarfism - Craniostenosis, Hartsfield syndromeAD/Digenic/Multigenic41232
FGFR2Apert syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome, Lacrimoauriculodentodigital syndrome, Beare-Stevenson cutis gyrata syndrome, Antley-Bixler syndrome without genital anomalies or disordered steroidogenesis, Craniofacial-skeletal-dermatological dysplasia, Crouzon syndrome, Bent bone dysplasiaAD47145
FGFR3Lacrimoauriculodentodigital syndrome, Muenke syndrome, Crouzon syndrome with acanthosis nigricans, Camptodactyly, tall stature, and hearing loss (CATSHL) syndrome, Achondroplasia, Hypochondroplasia, Thanatophoric dysplasia type 1, Thanatophoric dysplasia type 2, SADDANAD/AR4768
FHHereditary leiomyomatosis and renal cell cancerAD89161
FHL1*Myopathy with postural muscle atrophy, Emery-Dreifuss muscular dystrophy, Reducing bod myopathyXL1847
FKBP10Bruck syndrome type 2, Osteogenesis imperfecta type 3, Osteogenesis imperfecta type 4AR1727
FKBP14Ehlers-Danlos syndrome with progressive kyphoscoliosis, myopathy, and hearing lossAR44
FKRPMuscular dystrophy-dystroglycanopathyAR3199
FKTNMuscular dystrophy-dystroglycanopathy, Dilated cardiomyopathy (DCM), Muscular dystrophy-dystroglycanopathy (limb-girdle)AD/AR2851
FLNAFrontometaphyseal dysplasia, Osteodysplasty Melnick-Needles, Otopalatodigital syndrome type 1, Otopalatodigital syndrome type 2, Terminal osseous dysplasia with pigmentary defectsXL86209
FLNBLarsen syndrome (dominant), Atelosteogenesis type 1, Atelosteogenesis type 3, Spondylo-carpal-tarsal dyspasiaAD/AR3898
FOXH1Congenital heart malformations, HoloprosencephalyAD32
FOXL2Premature ovarian failure, Blepharophimosis, epicanthus inversus, and ptosisAD69203
FREM1Bifid nose, Manitoba oculotrichoanal syndrome, TrigonocephalyAD/AR823
GAAGlycogen storage diseaseAR79503
GBA*Gaucher diseaseAR73446
GBE1Glycogen storage diseaseAR2569
GDF5Multiple synostoses syndrome, Fibular hypoplasia and complex brachydactyly, Acromesomelic dysplasia, Hunter-Thompson, Symphalangism, proximal, Chondrodysplasia, Brachydactyly type A2, Brachydactyly type C, Grebe dysplasiaAD/AR2252
GFAPAlexander diseaseAD110112
GFPT1Myasthenic syndrome, congenitalAR633
GH1*Isolated growth hormone deficiency, Kowarski syndromeAD/AR2498
GHRGrowth hormone insensitivity syndrome (Laron syndrome)AD/AR32100
GHRHRIsolated growth hormone deficiencyAR1347
GJA1*Oculodentodigital dysplasia mild type, Oculodentodigital dysplasia severe type, Syndactyly type 3AD23103
GLE1Lethal congenital contracture syndrome, Arthrogryposis, lethal, with anterior horn cell diseaseAR49
GLI2Culler-Jones syndromeAD1674
GLI3Acrocallosal syndrome, Pallister-Hall syndrome, Grieg cephalopolysndactyly syndrome, Postaxial polydactyly type A, Preaxial polydactyly type 3, Preaxial polydactyly type 4AD49221
GMPPBMuscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), Limb-girdle muscular dystrophy-dystroglycanopathyAR1326
GNASMcCune-Albright syndrome, Progressive osseous heteroplasia, Pseudohypoparathyroidism, Albright hereditary osteodystrophyAD45257
GNPATRhizomelic chondrodysplasia punctata, rhizomelicAR814
GPC3Simpson-Golabi-Behmel syndromeXL2265
GPSM2Deafness, Chudley-McCullough syndromeAR1011
GRIA3Mental retardationXL917
HDAC8Cornelia de Lange syndromeXL1840
HEPACAMMegalencephalic leukoencephalopathy with subcortical cysts, remittingAD/AR923
HESX1Septooptic dysplasia, Pituitary hormone deficiency, combinedAR/AD1125
HOXA13Hand-foot-uterus syndrome, Hand-foot-genital syndrome, Guttmacher syndromeAD822
HOXD13Brachydactyly-syndactyly syndrome, Synopolydactyly, Syndactyly, Synopolydactyly with clefting, Brachydactyly type DAD/AR1838
HSPG2Schwartz-Jampel syndrome, Dyssegmental dysplasia Silverman-Handmaker type, Dyssegmental dysplasia Rolland-Desbuquis typeAD/AR1552
HUWE1Mental retardation, syndromic, TurnerXL831
IFT80Short -rib thoracic dysplasia with or without polydactyly, Asphyxiating thoracic dysplasia (ATD; Jeune)AR57
IFT122*Sensenbrenner syndrome, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 1, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 2AR913
IFT140Short -rib thoracic dysplasia with or without polydactyly, Asphyxiating thoracic dysplasia (ATD; Jeune)AR1446
IFT172Retinitis pigmentosa, Short -rib thoracic dysplasia with or without polydactyly, Asphyxiating thoracic dysplasia (ATD; Jeune)AR1821
IGF1Insulin-like growth factor I deficiencyAR412
IGF1RInsulin-like growth factor I, resistanceAD/AR562
IGFALSInsulin-like growth factor-binding protein, acid-labile subunit, deficiencyAR528
IHHAcrocapitofemoral dysplasia, Brachydactyly, Syndactyly type LuekenAD/AR1117
IKBKG*Incontinentia pigmenti, Ectodermal, dysplasia, anhidrotic, lymphedema and immunodeficiency, Immunodeficiency, Invasive pneumococcal disease, recurrent, isolated, Osteopetrosis with ectodermal dysplasia and immune defect (OLEDAID)XL30141
INSRHyperinsulinemic hypoglycemia, familial, Rabson-Mendenhall syndrome, Donohoe syndromeAD/AR35175
IRF6Orofacial cleft, Popliteal pterygium syndrome, van der Woude syndromeAD26327
IRS1Diabetes mellitus, noninsulin-dependentAD/AR223
ISPDMuscular dystrophy-dystroglycanopathyAR2042
KAT6BOhdo syndrome, SBBYS variant, Genitopatellar syndromeAD2353
KBTBD13Nemaline myopathyAD36
KDM6AKabuki syndromeXL1848
KIAA0196Spastic paraplegia, Ritscher-Schinzel syndrome (3C syndrome)AD/AR714
KIF1BPGoldberg-Shprintzen megacolon syndromeAR5
KIF7Acrocallosal syndrome, Hydrolethalus syndrome, Al-Gazali-Bakalinova syndrome, Joubert syndromeAR/Digenic1339
KITGastrointestinal stromal tumorAD27111
KLHL40Nemaline myopathyAR524
KMT2DKabuki syndromeAD136558
KRAS*Noonan syndrome, Cardiofaciocutaneous syndromeAD4638
KRIT1Cerebral cavernous malformationsAD22247
L1CAMMental retardation, aphasia, shuffling gait, and adducted thumbs (MASA) syndrome, Hydrocephalus due to congenital stenosis of aqueduct of Sylvius, Spastic, CRASH syndrome, Corpus callosum, partial agenesisXL37286
LAMA2Muscular dystrophy, congenital merosin-deficient, SchizophreniaAD/AR72225
LAMP2Danon diseaseXL4681
LARGEMuscular dystrophy-dystroglycanopathyAR1522
LBRPelger-Huet anomaly, Reynolds syndrome, Greenberg/HEM skeletal dysplasia, Hydrops-ectopic calcification-moth-eaten skeletal dysplasiaAD1522
LEMD3Buschke-Ollendorff syndrome, OsteopoikilosisAD929
LHX3Pituitary hormone deficiency, combinedAR914
LHX4Pituitary hormone deficiency, combinedAD917
LIFRStuve-Wiedemann dysplasia, Schwartz-Jampel type 2 syndromeAR928
LIG4Severe combined immunodeficiency with sensitivity to ionizing radiation, LIG4 syndromeAR836
LMNAHeart-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 typeAD/AR183458
LMX1BNail-patella syndromeAD18190
LRP4Cenani-Lenz syndactyly syndrome, Sclerosteosis, Myasthenic syndrome, congenitalAD/AR1223
LRP5*Van Buchem disease, Osteoporosis-pseudoglioma syndrome, Hyperostosis, endosteal, Osteosclerosis, Exudative vitreoretinopathy, Osteopetrosis late-onset form type 1, LRP5 primary osteoporosisAD/AR/Digenic36163
LTBP2Weill-Marchesani syndrome, Microspherophakia and/or megalocornea, with ectopia lentis and with or without secondary glaucoma, Glaucoma, primary congenitalAR2123
MASP13MC syndromeAR714
MATN3Spondyloepimetaphyseal dysplasia Matrilin type, Multiple epiphyseal dysplasia type 5 (EDM5)AD/AR825
MBD5Mental retardationAD2172
MED12Ohdo syndrome, Mental retardation, with Marfanoid habitus, FG syndrome, Opitz-Kaveggia syndrome, Lujan-Fryns syndromeXL1719
MEF2CMental retardationAD2566
MID1*Opitz GBBB syndromeXL1894
MITFRenal cell carcinoma with or without malignant melanoma, Tietz albinism-deafness syndrome, Waardenburg syndrome, Melanoma, cutaneous malignantAD1550
MLC1Megalencephalic leukoencephalopathy with subcortical cystsAR17111
MMP9Metaphyseal anadysplasiaAR112
MPZNeuropathy, Roussy-Levy syndrome, Dejerine-Sottas disease, Charcot-Marie-Tooth diseaseAD74235
MRE11AAtaxia-telangiectasia-like disorder-1AD2538
MSX2*Parietal foramina, Parietal foramina with cleidocranial dysplasia, Craniosynostosis Boston typeAD924
MTM1Myopathy, centronuclearXL152284
MUSKMyasthenic syndrome, congenitalAR1017
MYBPC1Arthrogryposis, Lethal congenital contractural syndromeAD/AR47
MYH2Inclusion body myopathyAD1020
MYH7Hypertrophic cardiomyopathy (HCM), Myopathy, myosin storage, Myopathy, distal, Dilated cardiomyopathy (DCM)AD/AR285748
NALCNNeuroaxonal neurodegeneration, infantile, with facial dysmophism, Congenital contractures of the limbs and face, hypotonia, and developmental delayAD/AR2328
NDE1Microhydranencephaly, LissencephalyAR1014
NEB*Nemaline myopathyAR34262
NEK1Short -rib thoracic dysplasia with or without polydactyly, SRPS type 2 (Majewski)AR/Digenic810
NF1*Watson syndrome, Neurofibromatosis, Neurofibromatosis-Noonan syndromeAD2612607
NF2Schwannomatosis, NeurofibromatosisAD24423
NHEJ1Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiationAR813
NIPBLCornelia de Lange syndromeAD246404
NODALHeterotaxy, visceralAD423
NOGTarsal-carpal coalition syndrome, Multiple synostosis syndrome, Stapes ankylosis with broad thumb and toes (Teunissen-Cremers syndrome), Symphalangism, proximal, Brachydactyly type B2AD1861
NOTCH1Aortic valve diseaseAD2872
NOTCH2*Alagille syndrome, Hajdu-Cheney syndromeAD2156
NPR2Acromesomelic dysplasia type Maroteaux, Epiphyseal chondrodysplasia, Miura, Short stature with nonspecific skeletal abnormalitiesAD/AR1461
NR5A1Adrenocortical insufficiency, Premature ovarian failure, 46,XY sex reversalAD/AR21137
NRG1Nonsyndromic Hirschsprung diseaseAD/AR116
NSD1Sotos syndrome, Weaver syndrome, Beckwith-Wiedemann syndromeAD212461
NSDHLCongenital hemidysplasia with ichthyosiform erythroderma and limb defects (CHILD syndrome), CK syndromeXL1528
OBSL13-M syndromeAR922
OCRLLowe syndrome, Dent diseaseXL33251
OFD1Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndromeXL129148
OPHN1Mental retardation, with cerebellar hypoplasia and distinctive facial appearanceXL1334
ORC1Meier-Gorlin syndrome (Ear-patella-short stature syndrome)AR99
ORC4Meier-Gorlin syndrome (Ear-patella-short stature syndrome)AR135
ORC6Meier-Gorlin syndrome (Ear-patella-short stature syndrome)AR55
OTX2Microphthalmia, syndromic, Pituitary hormone deficiency, combined, Retinal dystrophy, early-onset, and pituitary dysfunctionAD1665
P3H1Osteogenesis imperfectaAR1233
PAFAH1B1Lissencephaly, Subcortical laminar heterotopiaAD106165
PAPSS2Brachyolmia 4 with mild epiphyseal and metaphyseal changes, SEMD PAPPS2 typeAR1021
PAX3Craniofacial-deafness-hand syndrome, Waardenburg syndromeAD/AR20135
PAX6Aniridia, cerebellar ataxia, and mental retardation (Gillespie syndrome), Keratitis, Coloboma, ocular, Cataract with late-onset corneal dystrophy, Morning glory disc anomaly, Foveal hypoplasia, Aniridia, Optic nerve hypoplasia, Peters anomalyAD49461
PCNTMicrocephalic osteodysplastic primordial dwarfismAR3082
PDCD10Cerebral cavernous malformationsAD1076
PEX7Refsum disease, Rhizomelic CDP type 1AR1751
PHEXHypophosphatemic ricketsXL75411
PHF6Borjeson-Forssman-Lehmann syndromeXL1527
PIEZO2*Marden-Walker syndrome, Distal arthrogryposisAD2124
PIGA*Multiple congenital anomalies-hypotonia-seizures syndromeXL1914
PIK3CA*Cowden syndrome, CLOVESAD3044
PITX2Axenfeld-Rieger syndrome, Ring dermoid of cornea, Iridogoniodysgenesis, Peters anomalyAD1385
PLOD1Ehlers-Danlos syndromeAR1637
PLOD2Bruck syndrome, Osteogenesis imperfecta type 3AR411
PMM2Congenital disorder of glycosylationAR37119
PNKPEpileptic encephalopathy, early infantile, Ataxia-oculomotorAR2116
POLR1CTreacher Collins syndromeAR1318
POMGNT1Muscular dystrophy-dystroglycanopathyAR5573
POMT1Muscular dystrophy-dystroglycanopathyAR3181
POMT2Muscular dystrophy-dystroglycanopathyAR2848
PORDisordered steroidogenesis due to cytochrome p450 oxidoreductase deficiency, Antley-Bixler syndromeAR1284
POU1F1Pituitary hormone deficiency, combinedAR1942
PPIBOsteogenesis imperfecta type 2, Osteogenesis imperfecta type 3, Osteogenesis imperfecta type 4AR611
PQBP1Renpenning syndromeXL817
PRKAR1AMyxoma, intracardiac, Acrodysostosis, Pigmented nodular adrenocortical disease, Carney complexAD50173
PROP1Pituitary hormone deficiency, combinedAR1934
PTCH1Basal cell nevus syndromeAD46348
PTEN*Bannayan-Riley-Ruvalcaba syndrome, Lhermitte-Duclos syndrome, Cowden syndromeAD192564
PTH1RMetaphyseal chondrodysplasia Jansen type, Failure of tooth eruption, Eiken dysplasia, Blomstrand dysplasiaAD/AR1340
PTPN11LEOPARD syndrome, Noonan syndrome, MetachondromatosisAD122129
PYCR1Cutis laxa AR type 2BAR1234
RAB3GAP1Warburg micro syndromeAR1658
RAB3GAP2Warburg micro syndrome, Martsolf syndromeAR711
RAB39BWaisman parkinsonism-mental retardation syndrome, Mental retardationXL411
RAF1LEOPARD syndrome, Noonan syndrome, Dilated cardiomyopathy (DCM)AD3742
RAPSNMyasthenic syndrome, congenitalAR1857
RARS2Pontocerebellar hypoplasiaAR1730
RASA1Parkes Weber syndrome, Capillary malformation-arteriovenous malformation, Spinal arteriovenous anomaliesAD18113
RBBP8Seckel syndrome, Jawad syndromeAR45
RBPJ*Adams-Oliver syndromeAD23
RECQL4Baller-Gerold syndrome, RAPADILINO syndrome, Rothmund-Thomson syndromeAR3492
RELNLissencephaly, Epilepsy, familial temporal lobeAD/AR1731
RETHirschsprung disease, Central hypoventilation syndrome, congenital, Pheochromocytoma, Medullary thyroid carcinoma, Multiple endocrine neoplasiaAD/AR80405
RMRPCartilage-hair hypoplasia, Metaphyseal dysplasia without hypotrichosis, Anauxetic dysplasiaAR24119
RNU4ATACRoifman syndrome, Microcephalic osteodysplastic primordial dwarfism type 1, Microcephalic osteodysplastic primordial dwarfism type 3AR1518
ROR2Robinow syndrome recessive type, Brachydactyly type BAD/AR1837
RUNX2Cleidocranial dysplasia, Metaphyseal dysplasia with maxillary hypoplasiaAD19203
RYR1Central core disease, Malignant hyperthermia, Minicore myopathy with external ophthalmoplegia, Centronuclear myopathy, Minicore myopathy, Multicore myopathyAD/AR123563
SBDS*Aplastic anemia, Shwachman-Diamond syndrome, Severe spondylometaphyseal dysplasiaAD/AR1288
SCO2Leigh syndrome, Hypertrophic cardiomyopathy (HCM), Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency, MyopiaAD/AR1732
SELENONMuscular dystrophy, rigid spine, Myopathy, congenital, with fiber- disproportionAR1650
SERPINF1Osteogenesis imperfecta type 3, Osteogenesis imperfecta type 4AR729
SERPINH1Osteogenesis imperfecta type 3AR35
SF3B4Acrofacial dysostosis 1, NagerAD2533
SHHHoloprosencephaly, Microphthalmia with colobomaAD29212
SHOX*Leri-Weill dyschondrosteosis, Langer mesomelic dysplasia, Short statureXL/PAR23366
SIL1Marinesco-Sjogren syndromeAR1449
SIX5Branchiootorenal syndromeAD37
SKIShprintzen-Goldberg syndromeAD1520
SLC12A6Agenesis of the corpus callosum with peripheral neuropathy (Andermann syndrome)AR1217
SLC26A2Diastrophic dysplasia, Atelosteogenesis type 2, De la Chapelle dysplasia, Recessive Multiple Epiphyseal dysplasia, Achondrogenesis type 1BAR3251
SLC29A3Histiocytosis-lymphadenopathy plus syndrome, DysosteosclerosisAR1722
SLC34A3Hypophosphatemic rickets with hypercalciuriaAR1036
SLC39A13Spondylodysplastic Ehlers-Danlos syndromeAR27
SLCO2A1Hypertrophic osteoarthropathyAD/AR946
SMAD3Aneurysms-osteoarthritis syndrome, Loeys-Dietz syndromeAD2650
SMAD4Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Polyposis, juvenile intestinal, Myhre dysplasia, Hereditary hemorrhagic telangiectasiaAD119128
SMARCA2Nicolaides-Baraitser syndromeAD2467
SMARCA4Rhabdoid tumor predisposition syndromeAD1942
SMARCAL1Schimke immunoosseous dysplasiaAR970
SMARCB1Schwannomatosis, Rhabdoid tumor predisposition syndromeAD17115
SMC1ACornelia de Lange syndromeXL3954
SMC3Cornelia de Lange syndromeAD1416
SOS1Noonan syndromeAD4166
SOX2*Microphthalmia, syndromicAD2494
SOX9Campomelic dysplasia, 46,XY sex reversal, Brachydactyly with anonychia (Cooks syndrome)AD24135
SOX10Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung diseaseAD31119
SPRED1Legius syndromeAD1271
SRCAPFloating-Harbor syndromeAD724
SRPX2Rolandic epilepsy, mental retardation, and speech dyspraxiaXL13
SRY46,XX disorder of sex development, 46,XY disorder of sex developmentYL22102
STAT5B*Growth hormone insensitivity with immunodeficiencyAR511
SYN1Epilepsy, with variable learning disabilities and behavior disordersXL75
TBX3Ulnar-Mammary syndromeAD521
TBX19Adrenocorticotropic hormone deficiencyAR526
TCIRG1Osteopetrosis, severe neonatal or infantile forms (OPTB1)AR9127
TCOF1Treacher Collins syndromeAD17303
TCTN3Orofaciodigital syndrome (Mohr-Majewski syndrome), Joubert syndromeAR810
TGFB1Diaphyseal dysplasia Camurati-EngelmannAD1128
TGFB2Loeys-Dietz syndromeAD1524
TGFB3Loeys-Dietz syndrome (Reinhoff syndrome), Arrhythmogenic right ventricular dysplasiaAD818
TGFBR1Loeys-Dietz syndromeAD2567
TGFBR2Loeys-Dietz syndromeAD54130
TK2Mitochondrial DNA depletion syndromeAR3844
TMEM5Muscular dystrophy-dystroglycanopathyAR87
TMEM43Arrhythmogenic right ventricular dysplasia, Emery-Dreifuss muscular dystrophyAD515
TNFRSF11AFamilial expansile osteolysis, Paget disease of bone, Osteopetrosis, severe neonatal or infantile forms (OPTB1)AD/AR822
TNFRSF11BPaget disease of bone, juvenileAR821
TNNI2Arthrogryposis multiplex congenitaAD411
TNNT1Nemaline myopathyAR25
TNXB*Ehlers-Danlos syndromeAR826
TP63Rapp-Hodgkin syndrome, Orofacial cleft, ADULT syndrome, Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome, Ankyloblepharon-ectodermal defects-cleft lip/palate, Split-hand/foot malformation, Limb-mammary syndromeAD38114
TPM2CAP myopathy, Nemaline myopathy, Arthrogryposis, distalAD1137
TPM3*CAP myopathy, Nemaline myopathy, Myopathy, congenital, with fiber- disproportionAD1826
TRAPPC2*Spondyloepiphyseal dysplasia tardaXL1254
TRPS1Trichorhinophalangeal syndrome type 1, Trichorhinophalangeal syndrome type 3AD18127
TRPV4Metatropic dysplasia, Spondyloepiphyseal dysplasia Maroteaux type, Parastremmatic dwarfism, Hereditary motor and sensory neuropathy, Spondylometaphyseal dysplasia Kozlowski type, Spinal muscular atrophy, Charcot-Marie-Tooth disease, Brachyolmia (autosomal dominant type), Familial Digital arthropathy with brachydactylyAD5371
TSC1Lymphangioleiomyomatosis, Tuberous sclerosisAD61306
TSC2Lymphangioleiomyomatosis, Tuberous sclerosisAD141977
TSEN2Pontocerebellar hypoplasiaAR64
TSEN54Pontocerebellar hypoplasiaAR1620
TTC7AGastrointestinal defects and immunodeficiency syndromeAR1839
TTC21BShort-rib thoracic dysplasia, Nephronophthisis, Asphyxiating thoracic dysplasia (ATD; Jeune)AR647
TTRDystransthyretinemic hyperthyroxinemia, Amyloidosis, hereditary, transthyretin-relatedAD51138
TUBA8Polymicrogyria with optic nerve hypoplasiaAR11
TUBB2B*Polymicrogyria, asymmetricAD1229
TUBB3*Fibrosis of extraocular muscles, congenital, Cortical dysplasia, complex, with other brain malformationsAD/AR1823
TWIST1Saethre-Chotzen syndrome, Robinow-Sorauf syndrome, CraniosynostosisAD14188
TXNL4ABurn-McKeown syndromeAR1810
TYROBPNasu-Hakola disease, Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathyAR814
UBE2AMental retardation, syndromic, NascimentoXL421
UPF3BMental retardation, syndromicXL516
VDRVitamin D-dependent ricketsAD/AR1767
VLDLRCerebellar ataxia, mental retardation, and dysequilibrium syndromeAR921
VPS33BArthrogryposis - renal dysfunction - cholestasisAD/AR953
VRK1Pontocerebellar hypoplasiaAR68
WDR19Retinitis pigmentosa, Nephronophthisis, Short -rib thoracic dysplasia with or without polydactyly, Senior-Loken syndrome, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 1, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 2, Asphyxiating thoracic dysplasia (ATD; Jeune)AD/AR1625
WDR34Short -rib thoracic dysplasia with or without polydactyly, Asphyxiating thoracic dysplasia (ATD; Jeune)AR1015
WDR35Cranioectodermal dysplasia (Levin-Sensenbrenner) type 1, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 2, Short rib-polydactyly syndrome type 5AR1524
WISP3Arthropathy, progressive pseudorheumatoid, of childhood, Spondyloepiphyseal dysplasia tarda with progressive arthropathyAR1368
WNT5ARobinow syndromeAD55
WNT10AOdontoonychodermal dysplasia, Tooth agenesis, selective, Schopf-Schulz-Passarge syndromeAD/AR1070
YWHAEDistal 17p13.3 microdeletion syndrome, Endometrial stromal sarcoma, 17p13.3 microduplication syndrome, Miller-Dieker syndromeAD/AR1142
ZBTB42Lethal congenital contracture syndromeAR11
ZEB2*Mowat-Wilson syndromeAD104247
ZNF469Brittle cornea syndromeAR3135
  • * 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 (; HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, The list of associated (gene specific) phenotypes are generated from CDG ( or Orphanet ( databases.

GeneGenomic location HG19HGVSRefSeqRS-numberCommentReference
IFITM5Chr11:299504c.-14C>TNM_001025295.2rs587776916Explain almost all cases of OI type VPMID 23240094

Blueprint Genetics offers a Comprehensive Skeletal / Malformation Syndrome Panel that covers classical genes associated with malformations and skeletal syndromes. 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 (, the NHLBI GO Exome Sequencing Project (ESP;, the Exome Aggregation Consortium (ExAC;, ClinVar database of genotype-phenotype associations ( and the Human Gene Mutation Database ( The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (, Polyphen (, and Mutation Taster (

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


ICD codes

Commonly used ICD-10 codes when ordering the Comprehensive Skeletal / Malformation Syndrome Panel

Q87Skeletal syndromes

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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