3-M Syndrome / Primordial Dwarfism Panel

24 gene panel that includes assessment of non-coding variants

Ideal for patients with a clinical suspicion of primordial dwarfism including 3-M syndrome, Jawad syndrome and Meier-Gorlin syndrome microcephalic primordial dwarfism disorders (mopd, Seckel syndrome or short stature-onychodysplasia-facial dysmorphism-hypotrichosis syndrome). The genes on this panel are included in the Comprehensive Short Stature Panel and the Comprehensive Growth Disorders / Skeletal Dysplasias and Disorders Panel.

Analysis methods Availability Number of genes Test code CPT codes
PLUS
SEQ
DEL/DUP
4 weeks 24 GHC0112 DEL/DUP 81479
SEQ 81479

Summary

ICD codes
Commonly used ICD-10 code(s) when ordering the 3-M Syndrome / Primordial Dwarfism Panel

ICD-10 Disease
Q87.1 3-M syndrome
Q87.1 Microcephalic primordial dwarfism disorders (mopd)
Q87.1 Seckel syndrome
Q87.1 Meier-Gorlin syndrome (Ear-patella-short stature syndrome)
Q87.1 Jawad syndrome
Q87.1 Short stature-onychodysplasia-facial dysmorphism-hypotrichosis syndrome

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.

About

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 intellectual disability, but there can be significant clinical overlap among syndromes. Intellect is intact in most cases of microcephalic osteodysplastic primordial dwarfism type II (MOPD II) and Meier-Gorlin syndrome, whereas Seckel syndrome is classically characterized by substantial intellectual disability. The genetic bases of many of these disorders have been elucidated recently, and the implicated genes have been shown to be vital for fundamental biological processes, such as DNA replication and damage repair. Microcephalic primordial dwarfism constitutes a group of disorders characterized by severe pre- and postnatal growth retriction accompanied by microcephaly. These disorders include MOPD I (Taybi-Linder syndrome), II and III, various types of Seckel syndrome and Meier-Gorlin syndrome. Altogether 150 published cases of type I, II and III MOPD have been reported in the literature. 3-M syndrome is characterized by prenatal growth restriction in the absence of recognizable maternal or placental pathology and by the failure of postnatal catch-up growth resulting in significant proportionate short stature. It is estimated that 77.5% of 3-M syndrome is attributed to mutations in the CUL7 gene, 16% to mutations in OBSL1 gene and less than 5% to mutations in CCDC8 gene. This panel also includes other genes causing syndromes with prenatal-onset growth retardation.

Panel Content

Genes in the 3-M Syndrome / Primordial Dwarfism Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ATRCutaneous telangiectasia and cancer syndrome, Seckel syndromeAD/AR818
BCS1LBjornstad syndrome, GRACILE syndrome, Leigh syndrome, Mitochondrial complex III deficiency, nuclear type 1AR3337
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
CUL73-M syndrome, Yakut short stature syndromeAR2680
LARP7Alazami syndromeAR166
NOTCH2Alagille syndrome, Hajdu-Cheney syndromeAD3563
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
PCNTMicrocephalic osteodysplastic primordial dwarfismAR4884
POC1AShort stature, onychodysplasia, facial dysmorphism, and hypotrichosis (SOFT syndrome)AR48
RBBP8Seckel syndrome, Jawad syndromeAR66
RNU4ATACRoifman syndrome, Microcephalic osteodysplastic primordial dwarfism type 1, Microcephalic osteodysplastic primordial dwarfism type 3AR1521
RTTNMicrocephaly, short stature, and polymicrogyria with or without seizuresAR1310
SRCAPFloating-Harbor syndromeAD1340
TRIM37Mulibrey nanismAR1921
XRCC4Short stature, microcephaly, and endocrine dysfunctionAR911

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
BCS1LChr2:219524871c.-147A>GNM_004328.4
CUL7Chr6:43010511c.3897+29G>ANM_001168370.1
RBBP8Chr18:20581745c.2287+53T>GNM_002894.2
TRIM37Chr17:57106096c.1949-12A>GNM_015294.3
XRCC4Chr5:82400728c.-10-1G>TNM_022406.2rs869320678

Panel Update

Genes added

  • BCS1L
  • CCDC8
  • CDC45
  • LARP7
  • POC1A
  • RTTN
  • SRCAP
  • TRIM37
  • XRCC4

Genes removed

Test strength and Limitations

The strengths of this test include:

  • CAP and ISO-15189 accreditations covering all operations 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
  • 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

Our panels are sliced from our high-quality whole exome sequencing data.

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.

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.

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.