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Test Code
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5187
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Test Name
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Spondylo-Epi-Metaphyseal Dysplasias NGS Panel
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CPT Codes
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81479
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Expected Turnaround Time
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Typically 2 to 4 weeks from receipt of a sample in the laboratory. All cases involving ongoing pregnancies will be expedited.
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Clinical Utility
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Genetic analysis to provide a molecular diagnosis of this disorder. Recommended for individuals with a personal and/or family history of this disorder to ensure appropriate treatment and establish recurrence risk for family members.
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Specimen and Container Info
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Non-Prenatal Specimens Preferred/Alternate | Specimen Type | Containers | Volume | Preferred Specimen Type | Whole Blood | Lavender Top (EDTA) | 3 mL | Alternate Specimen Type | Genomic DNA | 1.5 mL Tube | 3 µg (at a concentration of at least 30 ng/µl), preferably in TE solution. | Alternate Specimen Type | Fibroblasts | T-25 Flasks | 2 confluent T-25 flasks, filled to capacity | Alternate Specimen Type | Saliva (Whole blood is recommended for CNV) | DNA Self-Collection Kit or Oragene Saliva Collection Kit for Young Children | Follow kit instructions (www.dnagenotek.com) |
Prenatal Specimens Either specimen type below is acceptable. Specimen Type | Containers | Volume | Cultured cells | T-25 Flasks | 2 confluent T-25 flasks derived from amnio or CVS samples. | Genomic DNA | 1.5 mL Tube | 3 µg (at a concentration of at least 30 ng/µl), preferably in TE solution. |
NOTE: For specimens from outside of North America, the preferred specimen type is Genomic DNA. HNL Genomics does not recommend shipping whole blood or cultured cells from any location other than the United States, Canada, or Mexico. |
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Transport Instructions
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- Transport at room temperature within 24 hours.
- If the specimen cannot be transported to the lab within 24 hours, refrigerate for up to 72 hours.
- Do not freeze or expose to extreme temperatures, refrigerate for up to 72 hours if cannot be transported to lab within 24 hours.
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Stability Requirements
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Room Temperature
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Refrigerated
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Causes for Rejection
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- Improperly labeled specimen (minimum of two patient identifiers)
- Inappropriate specimen type
- Incomplete or incorrect test request form
- Insufficient volume
- Specimen has leaked in transit
- Specimen without a test order
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Methodology
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Next Generation Sequencing and Copy Number Variation Analysis
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Performing Location
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Genomics - Snowdrift
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Alternate Names
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SEMD
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Description
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The Spondylo-Epi-Metaphyseal dysplasias NGS panel consists of fifty-four genes: ACAN, ACP5, B3GALT6, B3GAT3, BGN, C21orf2, CANT1, CHST3, COL2A1, COL9A1, COL9A2, COL9A3, COL10A1, COL11A1, COL11A2, COMP, DYM, DDR2, EIF2AK3, FGFR3, FLNB, FN1, GPX4, HSPG2, IDUA, IHH, IMPAD1, INPPL1, KIF22, LIFR, LONP1, MATN3, MMP9, MMP13, NANS, NEK1, NKX3-2, NPR2, PAPSS2, PAM16, PCYT1A, PTH1R, RAB33B, RMRP, RNU4ATAC, RSPRY1, RUNX2, SBDS, SLC26A2, SMARCAL1, TRAPPC2, TRPV4, WISP3, and XYLT1. It covers various chondrodysplasias with significant spinal, epiphyseal and/or metaphyseal involvement. Gene | Disorder | MIM | Inheritance | ACAN | Spondyloepimetaphyseal dysplasia, aggrecan type Spondyloepiphyseal dysplasia, Kimberley type Short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans | 612813 608361 165800 | AR AD AD | ACP5 | Spondyloenchondrodysplasia with immune dysregulation | 607944 | AR | B3GALT6 | Ehlers-Danlos syndrome, spondylodysplastic type, 2 Spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures | 615349 271640 | AR | B3GAT3 | Multiple joint dislocations, short stature, and craniofacial dysmorphism, with or without congenital heart defects | 245600 | AR | BGN | Spondyloepimetaphyseal dysplasia, X-linked | 300106 | XLR | C21orf2 | Axial spondylometaphyseal dysplasia Short-rib thoracic dysplasia, C21orf2 related | 602271 - | AR AR | CANT1 | Desbuquois dysplasia 1 | 251450 | AR | CHST3 | Spondyloepiphyseal dysplasia with congenital joint dislocations | 143095 | AR | COL2A1 | Type II collagenopathies | 108300, 132450 150600, 151210 156550, 183900 184250, 200610 271700, 604864 608805, 609162 609508, 616583 | AD | COL9A1 | Epiphyseal dysplasia, multiple, 6 Stickler syndrome, type IV | 614135 614134 | AD AR | COL9A2 | Epiphyseal dysplasia, multiple, 2 Stickler syndrome, type V | 600204 614284 | AD AR | COL9A3 | Epiphyseal dysplasia, multiple, 3 Stickler syndrome, COL9A3 related | 600969 | AD AR | COL10A1 | Metaphyseal chondrodysplasia, Schmid type | 156500 | AD | COL11A1 | Fibrochondrogenesis 1 Marshall syndrome Stickler syndrome, type II | 228520 154780 604841 | AR AD AD | COL11A2 | Fibrochondrogenesis 2 Otospondylomegaepiphyseal dysplasia Stickler syndrome, type III Weissenbacher-Zweymuller syndrome | 614524 215150 184840 277610 | AD/AR AR AD AD | COMP | Epiphyseal dysplasia, multiple, 1 Pseudoachondroplasia | 132400 177170 | AD AD | DDR2 | Spondylometaepiphyseal dysplasia, short limb-hand type | 271665 | AR | DYM | Dyggve-Melchior-Clausen disease Smith-McCort dysplasia | 223800 607326 | AR AR | EIF2AK3 | Epiphyseal dysplasia, multiple, with early-onset diabetes mellitus (Wolcott-Rallison syndrome) | 226980 | AR | FGFR3 | Achondroplasia Hypochondroplasia Thanatophoric dysplasia, type I Thanatophoric dysplasia, type II | 100800 146000 187600 187601 | AD AD AD AD | FLNB | FLNB related disorders | 108720, 108721 112310, 150250 272460 | AD/AR | FN1 | Spondylometaphyseal dysplasia, corner fracture type | 184255 | AD | GPX4 | Spondylometaphyseal dysplasia, Sedaghatian type | 250220 | AR | HSPG2 | Dyssegmental dysplasia, Silverman-Handmaker type Schwartz-Jampel syndrome, type 1 | 224410 255800 | AR AR | IDUA | Mucopolysaccharidosis Ih (Hurler) Mucopolysaccharidosis Ih/s (Hurler-Scheie) Mucopolysaccharidosis Is (Scheie) | 607014 607015 607016 | AR AR AR | IHH | Acrocapitofemoral dysplasia | 607778 | AR | IMPAD1 | Chondrodysplasia with joint dislocations, GPAPP type | 614078 | AR | INPPL1 | Opsismodysplasia | 258480 | AR | KIF22 | Spondyloepimetaphyseal dysplasia with joint laxity, type 2 | 603546 | AD | LIFR | Stuve-Wiedemann syndrome | 601559 | AR | LONP1 | CODAS syndrome | 600373 | AR | MATN3 | Epiphyseal dysplasia, multiple, 5 Spondyloepimetaphyseal dysplasia, MATN3 related | 607078 608728 | AD AR | MMP9 | Metaphyseal anadysplasia 2 | 613073 | AR | MMP13 | Metaphyseal anadysplasia 1 & Spondyloepimetaphyseal dysplasia, Missouri type Metaphyseal dysplasia, Spahr type | 602111 250400 | AD AR | NANS | Spondyloepimetaphyseal dysplasia, Genevieve type | 610442 | AR | NEK1 | Axial spondylometaphyseal dysplasia, NEK1 related Short-rib thoracic dysplasia 6 with or without polydactyly | - 263520 | AR AR / DR | NKX3-2 | Spondylo-megaepiphyseal-metaphyseal dysplasia | 613330 | AR | NPR2 | Acromesomelic dysplasia, Maroteaux type (AMDR) Epiphyseal chondrodysplasia, Miura type (ECDM) Short stature with nonspecific skeletal abnormalities (SNSK) | 602875 615923 616255 | AR AD AD | PAM16 | Spondylometaphyseal dysplasia, Megarbane-Dagher-Melike type | 613320 | AR | PAPSS2 | Brachyolmia 4 with mild epiphyseal and metaphyseal changes | 612847 | AR | PCYT1A | Spondylometaphyseal dysplasia with cone-rod dystrophy | 608940 | AR | PTH1R | Eiken syndrome Metaphyseal chondrodysplasia, Murk Jansen type | 600002 156400 | AR AD | RAB33B | Smith-McCort dysplasia 2 | 615222 | AR | RMRP | Anauxetic dysplasia Cartilage-hair hypoplasia Metaphyseal dysplasia without hypotrichosis | 607095 250250 250460 | AR AR AR | RNU4ATAC | Roifman syndrome | 616651 | AR | RSPRY1 | Spondyloepimetaphyseal dysplasia, Faden-Alkuraya type | 616723 | AR | RUNX2 | Cleidocranial dysplasia Metaphyseal dysplasia with maxillary hypoplasia with or without brachydactyly | 119600 156510 | AD AD | SBDS | Shwachman-Diamond syndrome | 260400 | AR | SLC26A2 | Achondrogenesis Ib, Atelosteogenesis II De la Chapelle dysplasia Diastrophic dysplasia Epiphyseal dysplasia, multiple, 4 | 600972 256050 256050 222600 226900 | AR AR AR AR AR | SMARCAL1 | Schimke immunoosseous dysplasia | 242900 | AR | TRAPPC2 | Spondyloepiphyseal dysplasia tarda | 313400 | XLR | TRPV4 | Metatropic dysplasia Parastremmatic dwarfism Spondyloepiphyseal dysplasia, Maroteaux type Spondylometaphyseal dysplasia, Kozlowski type | 156530 168400 184095 184252 | AD AD AD AD | WISP3 | Spondyloepiphyseal dysplasia tarda with progressive arthropathy | 208230 | AR | XYLT1 | Desbuquois dysplasia 2 | 615777 | AR |
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Testing Schedule
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Monday-Friday
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Genes
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ACAN, ACP5, B3GALT6, B3GAT3, BGN, C21orf2, CANT1, CHST3, COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3, COMP, DDR2, DYM, EIF2AK3, FGFR3, FLNB, FN1, GPX4, HSPG2, IDUA, IHH, IMPAD1, INPPL1, KIF22, LIFR, LONP1, MATN3, MMP13, MMP9, NANS, NEK1, NKX3-2, NPR2, PAM16, PAPSS2, PCYT1A, PTH1R, RAB33B, RMRP, RNU4ATAC, RSPRY1, RUNX2, SBDS, SLC26A2, SMARCAL1, TRAPPC2, TRPV4, WISP3, XYLT1
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Disease Group
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Skeletal Disorders
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