- Is a 98 gene panel that includes assessment of non-coding variants.
Is ideal for patients with a clinical suspicion of short stature and associated disorders.
The Blueprint Genetics Comprehensive Short Stature Syndrome Panel (test code MA2101):
Commonly used ICD-10 code(s) when ordering the Comprehensive Short Stature Syndrome Panel
|Q87.1||Meier-Gorlin syndrome (Ear-patella-short stature syndrome)|
|Q87.1||Short stature and associated syndromes|
|Q87.1||Microcephalic primordial dwarfism disorders (MOPD)|
|Q87.1||Short stature-onychodysplasia-facial dysmorphism-hypotrichosis syndrome|
- Blood (min. 1ml) in an EDTA tube
- Extracted DNA, min. 2 μg in TE buffer or equivalent
- Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)
Label the sample tube with your patient's name, date of birth and the date of sample collection.
We do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. In addition, if the patient is affected with a hematological malignancy, DNA extracted from a non-hematological source (e.g. skin fibroblasts) is strongly recommended.
Please note that, in rare cases, mitochondrial genome (mtDNA) variants may not be detectable in blood or saliva in which case DNA extracted from post-mitotic tissue such as skeletal muscle may be a better option.
Read more about our sample requirements here.
The clinical phenotypes of the disorders covered by this panel range in the severity of growth retardation and microcephaly, as well as in the degree of developmental delay, but there can be significant clinical overlap among syndromes. In addition to the disorders covered by the sub-panels, this comprehensive panel covers several other diseases associated with short stature, such as growth delay due to insulin-like growth factor I resistance or IGF1 deficiency (mutations in IGF1R and IGF1), hypothyroidism due to deficient transcription factors involved in pituitary development or function (HESX1, LHX3, LHX4, POU1F1 and PROP1), Rubinstein-Taybi syndrome (CREBBP and EP300), Cornelia de Lange syndrome (NIPBL, RAD21, SMC3, HDAC8 and SMC1A) and different forms of disproportionate short stature. Disproportionate short stature can manifest itself as short-limbed dwarfism or short-trunk dwarfism. Achondroplasia (autosomal dominant, mutations is FGFR3) is the most common form of disproportionate growth retardation, its estimated incidence is at about 1/25,000 live births worldwide. Identification of rare monogenic causes of short stature is critical since the genetic diagnosis may alert the clinician to other medical comorbidities for which the patient is at risk. For example, a male patient with 3-M syndrome will need to be monitored for the development of hypogonadism. Based on genetic studies in children with severe short stature of unknown etiology it has been suggested that monogenic causes of short stature are underdiagnosed in the pediatric endocrine clinic. Factors that increase the likelihood for a monogenic cause of short stature are severe GH deficiency, multiple pituitary hormone deficiency, unequivocal GH insensitivity, small for gestational age without catch-up growth, additional congenital anomalies or dysmorphic features, associated intellectual disability, microcephaly and height below −3 SD.
Genes in the Comprehensive Short Stature Syndrome Panel and their clinical significance
|ACTG1*||Deafness, Baraitser-Winter syndrome||AD||27||47|
|AMMECR1||Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis||XL||4||5|
|ARCN1||Rhizomelic short stature with microcephaly, micrognathia, and developmental delay (SRMMD)||AD||3||3|
|ATR||Cutaneous telangiectasia and cancer syndrome, Seckel syndrome||AD/AR||10||33|
|B3GAT3#*||Multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defects||AR||6||13|
|BCS1L||Bjornstad syndrome, GRACILE syndrome, Leigh syndrome, Mitochondrial complex III deficiency, nuclear type 1||AR||42||37|
|BRAF*||LEOPARD syndrome, Noonan syndrome, Cardiofaciocutaneous syndrome||AD||134||65|
|CBL||Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia||AD||24||43|
|CCDC8||Three M syndrome 3||AR||2||3|
|CDC45||Meier-Gorlin syndrome 7||AR||10||19|
|CDC6||Meier-Gorlin syndrome (Ear-patella-short stature syndrome)||AR||2||2|
|CDT1||Meier-Gorlin syndrome (Ear-patella-short stature syndrome)||AR||6||12|
|CENPJ||Seckel syndrome, Microcephaly||AR||34||9|
|CEP152||Seckel syndrome, Microcephaly||AR||20||20|
|CUL7||3-M syndrome, Yakut short stature syndrome||AR||26||83|
|DONSON||Microcephaly, short stature, and limb abnormalities (MISSLA), Microcephaly-Micromelia syndrome||10||19|
|FGD1||Aarskog-Scott syndrome, Mental retardation, syndromic||XL||29||51|
|FGFR3||Lacrimoauriculodentodigital 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, SADDAN||AD/AR||54||77|
|FN1||Glomerulopathy with fibronectin deposits 2||AD||14||25|
|GH1*||Isolated growth hormone deficiency, Kowarski syndrome||AD/AR||25||90|
|GHR||Growth hormone insensitivity syndrome (Laron syndrome)||AD/AR||35||115|
|GHRHR||Isolated growth hormone deficiency||AR||13||51|
|GNAS||McCune-Albright syndrome, Progressive osseous heteroplasia, Pseudohypoparathyroidism, Albright hereditary osteodystrophy||AD||64||274|
|HDAC8||Cornelia de Lange syndrome||XL||41||50|
|HESX1||Septooptic dysplasia, Pituitary hormone deficiency, combined||AR/AD||15||26|
|HRAS||Costello syndrome, Congenital myopathy with excess of muscle spindles||AD||43||31|
|IGF1||Insulin-like growth factor I deficiency||AR||4||8|
|IGF1R||Insulin-like growth factor I, resistance||AD/AR||12||64|
|IGFALS||Insulin-like growth factor-binding protein, acid-labile subunit, deficiency||AR||5||34|
|INSR||Hyperinsulinemic hypoglycemia, familial, Rabson-Mendenhall syndrome, Donohoe syndrome||AD/AR||44||190|
|IRS1||Diabetes mellitus, noninsulin-dependent||AD/AR||3||17|
|KRAS*||Noonan syndrome, Cardiofaciocutaneous syndrome||AD||63||35|
|LFNG#||Spondylocostal dysostosis, autosomal recessive 3||AR||1||5|
|LHX3||Pituitary hormone deficiency, combined||AR||9||16|
|LHX4||Pituitary hormone deficiency, combined||AD||10||23|
|LZTR1||Schwannomatosis, Noonan syndrome||AD/AR||34||71|
|NIPBL||Cornelia de Lange syndrome||AD||311||425|
|NOTCH2*||Alagille syndrome, Hajdu-Cheney syndrome||AD||37||70|
|ORC1||Meier-Gorlin syndrome (Ear-patella-short stature syndrome)||AR||9||10|
|ORC4||Meier-Gorlin syndrome (Ear-patella-short stature syndrome)||AR||24||6|
|ORC6||Meier-Gorlin syndrome (Ear-patella-short stature syndrome)||AR||7||6|
|OTX2||Microphthalmia, syndromic, Pituitary hormone deficiency, combined, Retinal dystrophy, early-onset, and pituitary dysfunction||AD||23||73|
|PCNT||Microcephalic osteodysplastic primordial dwarfism||AR||49||88|
|PITX2||Axenfeld-Rieger syndrome, Ring dermoid of cornea, Iridogoniodysgenesis, Peters anomaly||AD||23||101|
|POC1A||Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis (SOFT syndrome)||AR||4||8|
|POP1||Anauxetic dysplasia 2||AR||5||6|
|POU1F1||Pituitary hormone deficiency, combined||AR||20||41|
|PRMT7||Short stature, brachydactyly, intellectual developmental disability, and seizures (SBIDDS)||AR||10||11|
|PROP1||Pituitary hormone deficiency, combined||AR||33||37|
|PTPN11||Noonan syndrome, Metachondromatosis||AD||135||140|
|PUF60||Short stature, Microcephaly||AD||24||30|
|RAD21*||Cornelia de Lange syndrome 4||AD||14||11|
|RAF1||LEOPARD syndrome, Noonan syndrome, Dilated cardiomyopathy (DCM)||AD||45||53|
|RBBP8||Seckel syndrome, Jawad syndrome||AR||6||6|
|RNU4ATAC||Roifman syndrome, Microcephalic osteodysplastic primordial dwarfism type 1, Microcephalic osteodysplastic primordial dwarfism type 3||AR||15||24|
|RRAS||Noonan-syndrome like phenotype||AD/AR||2|
|RTTN||Microcephaly, short stature, and polymicrogyria with or without seizures||AR||16||16|
|SGMS2||Osteoporosis and osteoporotic fractures, Skeletal dysplasia and disorders||AD|
|SHOC2||Noonan-like syndrome with loose anagen hair||AD||2||4|
|SHOX#*||Leri-Weill dyschondrosteosis, Langer mesomelic dysplasia, Short stature||XL/PAR||25||431|
|SMC1A||Cornelia de Lange syndrome||XL||73||87|
|SMC3||Cornelia de Lange syndrome||AD||25||21|
|SOX11||Mental retardation, autosomal dominant 27||AD||11||14|
|STAT5B*||Growth hormone insensitivity with immunodeficiency||AR||9||13|
|TBX19||Adrenocorticotropic hormone deficiency||AR||12||27|
|TRMT10A||Microcephaly, short stature, and impaired glucose metabolism 1||AR||2||7|
|XRCC4||Short stature, microcephaly, and endocrine dysfunction||AR||9||10|
* Some, or all, of the gene is duplicated in the genome. Read more.
# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads), and/or the gene has exons listed under Test limitations section that are not included in the panel as they are not sufficiently covered with high quality sequence reads.
The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)
Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), mitochondrial (mi), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the 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 CGD or Mitomap databases.
Non-coding variants covered by Comprehensive Short Stature Syndrome Panel
|Gene||Genomic location HG19||HGVS||RefSeq||RS-number|
- CAP accredited laboratory
- CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
- Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
- Careful construction of clinically effective and scientifically justified gene panels
- Some of the panels include the whole mitochondrial genome (please see the Panel Content section)
- Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
- Our publicly available analytic validation demonstrating complete details of test performance
- ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants covered by this panel’ in the Panel Content section)
- Our rigorous variant classification scheme
- Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
- Our comprehensive clinical statements
The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: B3GAT3 (NM_001288722:5), SHOX (NM_006883:6). Genes with suboptimal coverage in our assay are marked with number sign (#) and genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. Gene is considered to have suboptimal coverage when >90% of the gene's target nucleotides are not covered at >20x with mapping quality score (MQ>20) reads. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).
- Complex inversions
- Gene conversions
- Balanced translocations
- Some of the panels include the whole mitochondrial genome but not all (please see the Panel Content section)
- Repeat expansion disorders unless specifically mentioned
- Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).
- Low level mosaicism in nuclear genes (variant with a minor allele fraction of 14.6% is detected with 90% probability)
- Stretches of mononucleotide repeats
- Low level heteroplasmy in mtDNA (>90% are detected at 5% level)
- Indels larger than 50bp
- Single exon deletions or duplications
- Variants within pseudogene regions/duplicated segments
- Some disease causing variants present in mtDNA are not detectable from blood, thus post-mitotic tissue such as skeletal muscle may be required for establishing molecular diagnosis.
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.
The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.
Our panels are sectioned from our high-quality, clinical grade NGS assay. Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table).
Assays have been validated for various sample types including EDTA-blood, isolated DNA (excluding from formalin fixed paraffin embedded tissue), saliva and dry blood spots (filter cards). These sample types were selected in order to maximize the likelihood for high-quality DNA yield. The diagnostic yield varies depending on the assay used, referring healthcare professional, hospital and country. Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. Blueprint Genetics’ Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis.
Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.
|Sensitivity % (TP/(TP+FN)||Specificity %|
|Single nucleotide variants||99.89% (99,153/99,266)||>99.9999%|
|Insertions, deletions and indels by sequence analysis|
|1-10 bps||99.2% (7,745/7,806)||>99.9999%|
|11-50 bps||99.13% (2,524/2,546)||>99.9999%|
|Copy number variants (exon level dels/dups)|
|1 exon level deletion (heterozygous)||100% (20/20)||NA|
|1 exon level deletion (homozygous)||100% (5/5)||NA|
|1 exon level deletion (het or homo)||100% (25/25)||NA|
|2-7 exon level deletion (het or homo)||100% (44/44)||NA|
|1-9 exon level duplication (het or homo)||75% (6/8)||NA|
|Simulated CNV detection|
|5 exons level deletion/duplication||98.7%||100.00%|
|Size range (0.1-47 Mb)||100% (25/25)|
|The performance presented above reached by Blueprint Genetics high-quality, clinical grade NGS sequencing assay with the following coverage metrics|
|Mean sequencing depth||143X|
|Nucleotides with >20x sequencing coverage (%)||99.86%|
Performance of Blueprint Genetics Mitochondrial Sequencing Assay.
|Sensitivity % (TP/(TP+FN)||Specificity|
|ANALYTIC VALIDATION (NA samples; n=4)|
|Single nucleotide variants|
|Heteroplasmic (45-100%)||100.0% (50/50)||100.0%|
|Heteroplasmic (35-45%)||100.0% (87/87)||100.0%|
|Heteroplasmic (25-35%)||100.0% (73/73)||100.0%|
|Heteroplasmic (15-25%)||100.0% (77/77)||100.0%|
|Heteroplasmic (10-15%)||100.0% (74/74)||100.0%|
|Heteroplasmic (5-10%)||100.0% (3/3)||100.0%|
|Heteroplasmic (<5%)||50.0% (2/4)||100.0%|
|CLINICAL VALIDATION (n=76 samples)|
|Single nucleotide variants n=2084 SNVs|
|Heteroplasmic (45-100%)||100.0% (1940/1940)||100.0%|
|Heteroplasmic (35-45%)||100.0% (4/4)||100.0%|
|Heteroplasmic (25-35%)||100.0% (3/3)||100.0%|
|Heteroplasmic (15-25%)||100.0% (3/3)||100.0%|
|Heteroplasmic (10-15%)||100.0% (9/9)||100.0%|
|Heteroplasmic (<5%)||88.7% (47/53)||99.93%|
|Insertions and deletions by sequence analysis n=42 indels|
|Heteroplasmic (45-100%) 1-10bp||100.0% (32/32)||100.0%|
|Heteroplasmic (5-45%) 1-10bp||100.0% (3/3)||100.0%|
|Heteroplasmic (<5%) 1-10bp||100.0% (5/5)||>0.9999|
|SIMULATION DATA /(mitomap mutations)|
|Insertions, and deletions 1-24 bps by sequence analysis; n=17|
|Homoplasmic (100%) 1-24bp||100.0% (17/17)||99.98%|
|Heteroplasmic (50%)||100.0% (17/17)||99.99%|
|Heteroplasmic (25%)||100.0% (17/17)||100.0%|
|Heteroplasmic (20%)||100.0% (17/17)||100.0%|
|Heteroplasmic (15%)||100.0% (17/17)||100.0%|
|Heteroplasmic (10%)||94.1% (16/17)||100.0%|
|Heteroplasmic (5%)||94.1% (16/17)||100.0%|
|Copy number variants (separate artifical mutations; n=1500)|
|Homoplasmic (100%) 500 bp, 1kb, 5 kb||100.0%||100.0%|
|Heteroplasmic (50%) 500 bp, 1kb, 5 kb||100.0%||100.0%|
|Heteroplasmic (30%) 500 bp, 1kb, 5 kb||100.0%||100.0%|
|Heteroplasmic (20%) 500 bp, 1kb, 5 kb||99.7%||100.0%|
|Heteroplasmic (10%) 500 bp, 1kb, 5 kb||99.0%||100.0%|
|The performance presented above reached by following coverage metrics at assay level (n=66)|
|Mean of medians||Median of medians|
|Mean sequencing depth MQ0 (clinical)||18224X||17366X|
|Nucleotides with >1000x MQ0 sequencing coverage (%) (clinical)||100%|
|rho zero cell line (=no mtDNA), mean sequencing depth||12X|
The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding and regulatory variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. If the test includes the mitochondrial genome the target region gene list contains the mitochondrial genes. 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. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases including, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with suboptimal coverage (<20X for nuclear genes and <1000X for mtDNA) if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.
We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.
Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.
The final step in the analysis is orthogonal confirmation. Sequence and copy number variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing by orthogonal methods such as qPCR/ddPCR when they do not meet our stringent NGS quality metrics for a true positive call.
Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references, abstracts and variant databases used to help ordering providers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.
Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.
Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. Our laboratory is therefore well-positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.