Comprehensive Short Stature Syndrome Panel

75 gene panel that includes assessment of non-coding variants

Ideal for patients with a clinical suspicion of short stature and associated disorders.

Analysis methods Availability Number of genes Test code CPT codes
4 weeks 75 GHC0120 SEQ 81404
SEQ 81405
SEQ 81406
DEL/DUP 81479


ICD codes
Commonly used ICD-10 code(s) when ordering the Comprehensive Short Stature Syndrome Panel

ICD-10 Disease
Q87.1 Short stature and associated syndromes

Sample requirements:

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • 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.


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.

Panel Content

Genes in the Comprehensive Short Stature Syndrome Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ACTBBaraitser-Winter syndromeAD4654
ACTG1Deafness, Baraitser-Winter syndromeAD2543
ATRCutaneous telangiectasia and cancer syndrome, Seckel syndromeAD/AR818
B3GAT3Multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defectsAR513
BCS1LBjornstad syndrome, GRACILE syndrome, Leigh syndrome, Mitochondrial complex III deficiency, nuclear type 1AR3337
BRAFLEOPARD syndrome, Noonan syndrome, Cardiofaciocutaneous syndromeAD13565
CBLNoonan syndrome-like disorder with or without juvenile myelomonocytic leukemiaAD2338
CCDC8Three M syndrome 3AR23
CDC6Meier-Gorlin syndrome (Ear-patella-short stature syndrome)AR22
CDC45Meier-Gorlin syndrome 7AR1019
CDT1Meier-Gorlin syndrome (Ear-patella-short stature syndrome)AR611
CENPJSeckel syndrome, MicrocephalyAR329
CEP63Seckel syndromeAR72
CEP152Seckel syndrome, MicrocephalyAR1920
CREBBPRubinstein-Taybi syndromeAD156348
CUL73-M syndrome, Yakut short stature syndromeAR2680
DHCR7Smith-Lemli-Opitz syndromeAR67216
EP300Rubinstein-Taybi syndromeAD5791
FGD1Aarskog-Scott syndrome, Mental retardation, syndromicXL2649
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/AR5372
GH1Isolated growth hormone deficiency, Kowarski syndromeAD/AR2586
GHRGrowth hormone insensitivity syndrome (Laron syndrome)AD/AR35109
GHRHRIsolated growth hormone deficiencyAR1343
GLI2Culler-Jones syndromeAD2676
GNASMcCune-Albright syndrome, Progressive osseous heteroplasia, Pseudohypoparathyroidism, Albright hereditary osteodystrophyAD62265
HDAC8Cornelia de Lange syndromeXL3344
HESX1Septooptic dysplasia, Pituitary hormone deficiency, combinedAR/AD1426
HRASCostello syndrome, Congenital myopathy with excess of muscle spindlesAD4129
IGF1Insulin-like growth factor I deficiencyAR48
IGF1RInsulin-like growth factor I, resistanceAD/AR1261
IGFALSInsulin-like growth factor-binding protein, acid-labile subunit, deficiencyAR533
INSRHyperinsulinemic hypoglycemia, familial, Rabson-Mendenhall syndrome, Donohoe syndromeAD/AR44183
IRS1Diabetes mellitus, noninsulin-dependentAD/AR316
KRASNoonan syndrome, Cardiofaciocutaneous syndromeAD6134
LARP7Alazami syndromeAR166
LHX3Pituitary hormone deficiency, combinedAR916
LHX4Pituitary hormone deficiency, combinedAD1023
LZTR1Schwannomatosis, Noonan syndromeAD2764
MAP2K1Cardiofaciocutaneous syndromeAD4521
MAP2K2Cardiofaciocutaneous syndromeAD2135
NIPBLCornelia de Lange syndromeAD290419
NOTCH2Alagille syndrome, Hajdu-Cheney syndromeAD3563
NRASNoonan syndromeAD3114
OBSL13-M syndromeAR1333
ORC1Meier-Gorlin syndrome (Ear-patella-short stature syndrome)AR99
ORC4Meier-Gorlin syndrome (Ear-patella-short stature syndrome)AR226
ORC6Meier-Gorlin syndrome (Ear-patella-short stature syndrome)AR76
OTX2Microphthalmia, syndromic, Pituitary hormone deficiency, combined, Retinal dystrophy, early-onset, and pituitary dysfunctionAD2168
PCNTMicrocephalic osteodysplastic primordial dwarfismAR4884
PITX2Axenfeld-Rieger syndrome, Ring dermoid of cornea, Iridogoniodysgenesis, Peters anomalyAD2396
POC1AShort stature, onychodysplasia, facial dysmorphism, and hypotrichosis (SOFT syndrome)AR48
POU1F1Pituitary hormone deficiency, combinedAR1941
PROP1Pituitary hormone deficiency, combinedAR2737
PTPN11Noonan syndrome, MetachondromatosisAD128139
RAD21Cornelia de Lange syndrome 4AD911
RAF1LEOPARD syndrome, Noonan syndrome, Dilated cardiomyopathy (DCM)AD4448
RASA2Noonan syndromeAD13
RBBP8Seckel syndrome, Jawad syndromeAR66
RIT1Noonan syndromeAD2025
RNU4ATACRoifman syndrome, Microcephalic osteodysplastic primordial dwarfism type 1, Microcephalic osteodysplastic primordial dwarfism type 3AR1521
RRASNoonan-syndrome like phenotypeAD/AR2
RTTNMicrocephaly, short stature, and polymicrogyria with or without seizuresAR1310
SHOC2Noonan-like syndrome with loose anagen hairAD24
SHOXLeri-Weill dyschondrosteosis, Langer mesomelic dysplasia, Short statureXL/PAR25426
SMC1ACornelia de Lange syndromeXL5687
SMC3Cornelia de Lange syndromeAD2120
SOS1Noonan syndromeAD4567
SOX2Microphthalmia, syndromicAD31100
SRCAPFloating-Harbor syndromeAD1340
STAT5BGrowth hormone insensitivity with immunodeficiencyAR810
TBX3Ulnar-Mammary syndromeAD620
TBX19Adrenocorticotropic hormone deficiencyAR827
TRIM37Mulibrey nanismAR1921
XRCC4Short stature, microcephaly, and endocrine dysfunctionAR911

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number

Panel Update

Genes added

  • ACTB
  • ACTG1
  • B3GAT3
  • BCS1L
  • BRAF
  • CBL
  • CCDC8
  • CDC45
  • GNAS
  • HDAC8
  • HRAS
  • LARP7
  • LZTR1
  • MAP2K1
  • MAP2K2
  • NRAS
  • POC1A
  • RAD21
  • RASA2
  • RIT1
  • RRAS
  • RTTN
  • SHOC2
  • SMC3
  • TRIM37
  • XRCC4

Genes removed

  • AKT1
  • BMP2
  • BMP4
  • BMPR1A
  • EYA1
  • FGF3
  • FOXL2
  • NR5A1
  • PTCH1
  • SHH
  • SIX3
  • TGIF1
  • ZIC2

Test strength and Limitations

The strengths of this test include:

  • CAP and ISO-15189 accreditations covering all operations at GHC Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • 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
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in GHC WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: *PPA2* (11, 12). 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. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • 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).

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

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

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

Test Performance

The GHC Genetics panel covers classical genes associated with Brugada syndrome, catecholaminergic polymorphic ventricular tachycardia (CPVT), cardiac arrest underlying cardiac condition, cardiac arrest cause unspecified, syncope and collapse, abnormal ECG, Long QT syndrome, arrhythmogenic right ventricular cardiomyopathy (ARVC) and Short QT syndrome. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. GHC Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient’s phenotype is suggestive of a specific mutation type.

Performance of GHC Genetics Whole Exome Sequencing (WES) assay.
All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
The performance presented above reached by WES with the following coverage metrics
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Detection of Del/Dup of several genes is by MLPA analysis (MS Holland). All genes are performed by CNV analysis through the genome depending on exon size, sequencing coverage and sequence content. We have validated the assays for different starting materials including isolated DNA from EDTA blood that provide high-quality results.

Bioinformatics & clinical interpretation

The sequencing data generated in our laboratory is analysed by our bioinformatic pipeline, integrating state-of-the art algorithms and industry-standard software solutions. We use also JSI medical systems software for sequencing data analysis. JSI medical systems is a certified system offering sophisticated bioinformatic software solutions covering a wide field of sequencing techniques.

Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results.

Every pathogenic or probably pathogenic variant is confirmed by the Sanger sequencing method. 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. The analysis of detected variants was performed on the basis of the reference database of polymorphisms and international mutation databases: UMD, LOVD and ClinVar.

The consequence of variants in coding and splice regions are estimated using Alamut software. The Alamut database contains more than 28000 coding genes, non-protein coding genes and pseudogenes. This database (shared with the high throughput annotation engine for NGS data, Alamut Batch) is frequently updated. Information comes from different public databases such as NCBI, EBI, and UCSC, as well as other sources including gnomAD, ESP, Cosmic, ClinVar, or HGMD and CentoMD (for those a separate subscription from Qiagen/Biobase and Centogene respectively is required). Alamut Visual finds information about nucleotide conservation data through many vertebrates’ species, with the phastCons and phyloP scores, amino acid conservation data through orthologue alignments and information on protein domains.

Moreover, we integrate several missense variant pathogenicity prediction tools and algorithms such as SIFT, PolyPhen, AlignGVGD or MutationTaster. It also offers a window dedicated to the in silico study of variants’ effect on RNA splicing, allowing the assessment of their potential impact on splice junctions and visualization of cryptic or de novo splice sites. Impact on splicing regulation is also assessed.

Clinical interpretation

At GHC 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 report. We recommend an interpretation of the findings of this molecular genetic analysis, including subsequent oncological consultation for the patient in the context of genetic counselling for the patient.

We strive to continuously monitor current genetic literature identifying new relevant information and findings and adapting them to our diagnostics. This enables relevant novel discoveries to be rapidly translated and adopted into our ongoing diagnostics development without delay. The undertaking of such comprehensive due diligence ensures that our diagnostic panels and clinical statements are the most up-to-date on the market.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. 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 analysed at our laboratories enables us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant three times at GHC Genetics. Reported variants of uncertain significance (VUS) are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size >10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at GHC Genetics.

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 used, and mutation databases to help our customers 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 within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counselling.

Our Clinical interpretation team analyses millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratories are therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by GHC Genetics is re-classified, our laboratories will issue a follow-up statement to the original ordering health care provider at no additional cost.