Arthrogryposes Panel

73 gene panel that includes assessment of non-coding variants

Ideal for patients with a clinical suspicion of arthrogryposis or fetal akinesia.

Analysis methods Availability Number of genes Test code CPT codes
PLUS
SEQ
DEL/DUP
4 weeks 73 GHC0114 SEQ 81404
SEQ 81405
SEQ 81406
DEL/DUP 81479

Summary

ICD codes
Commonly used ICD-10 code(s) when ordering the Brugada Syndrome Panel

ICD-10 Disease
Q74.3 Arthrogryposis

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

Arthrogryposis (also known as arthrogryposis multiplex congenita, AMC) is characterized by congenital contractures of 2 or more different body areas without a primary neurologic or muscle disease. Children born with joint contractures have abnormal fibrosis of the muscle tissue causing muscle shortening, and therefore are unable to perform passive extension and flexion in the affected joints. Arthrogryposis has been divided into three groups: amyoplasia, distal arthrogryposis, and syndromic. Amyoplasia is characterized by severe joint contractures and muscle weakness while distal arthrogryposis mainly involves the hands and feet. Syndromic arthrogryposis consists with a primary neurological or muscle disease. 70-80% of arthrogryposes are caused by neurological abnormalities and most types that have primary neurological or muscle disease result from an underlying genetic syndrome. More than 35 specific genetic disorders associated with arthrogryposis have been described. Fetal akinesia deformation sequence syndrome (FADS) is characterised by decreased fetal movement (fetal akinesia) as well as intrauterine growth restriction, arthrogryposis, and developmental anomalies.

Panel Content

Genes in the Arthrogryposes Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ACTA1MyopathyAD/AR61206
ADGRG6Lethal congenital contracture syndrome 9AR43
AGRNMyasthenic syndrome, congenitalAR1213
BIN1Myopathy, centronuclearAR715
CASKMental retardation and microcephaly with pontine and cerebellar hypoplasia, FG syndrome, Mental retardationXL80104
CFL2Nemaline myopathyAR36
CHATMyasthenic syndrome, congenitalAR2673
CHRNA1Myasthenic syndrome, congenitalAD/AR2934
CHRNB1Myasthenic syndromeAD/AR1010
CHRNDMyasthenic syndromeAD/AR1723
CHRNEMyasthenic syndromeAD/AR42129
CHRNGMultiple pterygium syndrome, Escobar syndromeAR1633
CHST14Ehlers-Danlos syndrome, musculocontracturalAR1421
CHUKCocoon syndromeAR23
CNTNAP1Lethal congenital contracture syndrome 7AR911
COL6A2Epilepsy, progressive myoclonic, Bethlem myopathy, Myosclerosis, congenital, Ullrich congenital muscular dystrophyAD/AR93159
COLQMyasthenic syndrome, congenitalAR1967
DHCR24DesmosterolosisAR68
DOK7Myasthenic syndrome, congenitalAR2271
DPAGT1Congenital disorder of glycosylation, Myasthenic syndrome, congenitalAR1730
ECEL1ArthrogryposisAR2529
EGR2Neuropathy, Dejerine-Sottas disease, Charcot-Marie-Tooth diseaseAD/AR1321
ERBB3Lethal congenital contractural syndrome 2AR114
ERCC5Xeroderma pigmentosum, Xeroderma pigmentosum/Cockayne syndromeAR2152
ERCC6Xeroderma Pigmentosum-Cockayne Syndrome, De Sanctis-Cacchione syndromeAD/AR5293
EXOSC3Pontocerebellar hypoplasiaAR1219
FBN2Congenital contractural arachnodactyly (Beals syndrome)AD4595
FHL1Myopathy with postural muscle atrophy, Emery-Dreifuss muscular dystrophy, Reducing bod myopathyXL2260
FKBP10Bruck syndrome type 2, Osteogenesis imperfecta type 3, Osteogenesis imperfecta type 4AR2037
FKTNMuscular dystrophy-dystroglycanopathy, Dilated cardiomyopathy (DCM), Muscular dystrophy-dystroglycanopathy (limb-girdle)AD/AR3457
FLVCR2Proliferative vasculopathy and hydraencephaly-hydrocephaly syndromeAR1016
GBAGaucher diseaseAR84471
GBE1Glycogen storage diseaseAR3470
GFPT1Myasthenic syndrome, congenitalAR942
GLE1Lethal congenital contracture syndrome, Arthrogryposis, lethal, with anterior horn cell diseaseAR716
KAT6BOhdo syndrome, SBBYS variant, Genitopatellar syndromeAD3862
KLHL40Nemaline myopathyAR726
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/AR231553
MPZNeuropathy, Roussy-Levy syndrome, Dejerine-Sottas disease, Charcot-Marie-Tooth diseaseAD99240
MTM1Myopathy, centronuclearXL153292
MUSKMyasthenic syndrome, congenitalAR1418
MYBPC1Arthrogryposis, Lethal congenital contractural syndromeAD/AR76
MYH2Inclusion body myopathyAD1722
MYH3ArthrogryposisAD2135
MYH8Carney complex variant, Arthrogryposis, distal, type 7, Trismus-pseudocamptodactyly syndromeAD11
NALCNNeuroaxonal neurodegeneration, infantile, with facial dysmophism, Congenital contractures of the limbs and face, hypotonia, and developmental delayAD/AR4441
NEBNemaline myopathyAR103289
PIEZO2Marden-Walker syndrome, Distal arthrogryposisAD3026
PLOD2Bruck syndrome, Osteogenesis imperfecta type 3AR817
PMM2Congenital disorder of glycosylationAR62127
RAPSNMyasthenic syndrome, congenitalAR2358
RARS2Pontocerebellar hypoplasiaAR2333
RIPK4Popliteal pterygium syndrome, lethal type, Bartsocas-Papas syndromeAR415
SCO2Leigh syndrome, Hypertrophic cardiomyopathy (HCM), Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency, MyopiaAR4233
SELENONMuscular dystrophy, rigid spine, Myopathy, congenital, with fiber- disproportionAR3262
SMN1Spinal muscular atrophyAR27111
SMN2Spinal muscular atrophyAD19
TGFB3Loeys-Dietz syndrome (Reinhoff syndrome), Arrhythmogenic right ventricular dysplasiaAD1722
TK2Mitochondrial DNA depletion syndromeAR3845
TNNI2Arthrogryposis multiplex congenitaAD511
TNNT1Nemaline myopathyAR37
TNNT3Arthyrgryposis, distal, type 2BAD33
TPM2CAP myopathy, Nemaline myopathy, Arthrogryposis, distalAD1738
TPM3CAP myopathy, Nemaline myopathy, Myopathy, congenital, with fiber- disproportionAD2227
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 brachydactylyAD6076
TSEN2Pontocerebellar hypoplasiaAR84
TSEN54Pontocerebellar hypoplasiaAR2121
UBA1Spinal muscular atrophy, infantileXL34
VIPAS39Arthrogryposis, renal dysfunction, and cholestasis 2AR813
VPS33BArthrogryposis - renal dysfunction - cholestasisAD/AR1658
VRK1Pontocerebellar hypoplasiaAR69
ZBTB42Lethal congenital contracture syndromeAR21
ZC4H2Wieacker-Wolff syndromeXL1914

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
CHRNEChr17:4806452c.-94G>ANM_000080.3
CHRNEChr17:4806453c.-95G>ANM_000080.3
CHRNEChr17:4806454c.-96C>TNM_000080.3rs748144899
CHRNEChr17:4804936c.501-16G>ANM_000080.3
COL6A2Chr21:47541407c.1459-63G>ANM_001849.3
ERCC6Chr10:50681659c.2599-26A>GNM_000124.3rs4253196
EXOSC3Chr9:37782146c.475-12A>GNM_016042.3rs370087266
FBN2Chr5:127671284c.3725-15A>GNM_001999.3
FBN2Chr5:127670560c.3974-24A>CNM_001999.3
FBN2Chr5:127670562c.3974-26T>GNM_001999.3
FKTNChr9:108368857c.648-1243G>TNM_006731.2
GBE1Chr3:81542963c.2053-3358_2053-3350delGTGTGGTGGinsTGTTTTTTACATGACAGGTNM_000158.3
LMNAChr1:156107037c.1608+14G>ANM_170707.3
LMNAChr1:156107433c.1609-12T>GNM_170707.3rs267607582
LMNAChr1:156100609c.513+45T>GNM_170707.3
LMNAChr1:156105681c.937-11C>GNM_170707.3rs267607645
MTM1ChrX:149808833c.529-909A>GNM_000252.2
MTM1ChrX:149818176c.868-13T>ANM_000252.2
NEBChr2:152355017c.24220-151C>ANM_001271208.1
PMM2Chr16:8898599c.179-25A>GNM_000303.2rs760689221
PMM2Chr16:8941558c.640-23A>GNM_000303.2
RAPSNChr11:47470715c.-199C>GNM_005055.4
RAPSNChr11:47470726c.-210A>GNM_005055.4rs786200905
RAPSNChr11:47469717c.193-15C>ANM_005055.4
RARS2Chr6:88244587c.613-3927C>TNM_020320.3
SELENONChr1:26143316c.*1107T>CNM_020451.2
TGFB3Chr14:76425035c.*495C>TNM_003239.2rs387906514
TGFB3Chr14:76447266c.-30G>ANM_003239.2rs770828281
VPS33BChr15:91550814c.499-11G>ANM_018668.3

Panel Update

Genes added

  • ADGRG6
  • CHUK
  • CNTNAP1
  • ERBB3
  • FKBP10
  • FLVCR2
  • LMNA
  • MYH8
  • RIPK4
  • SMN1
  • SMN2
  • TNNT3
  • UBA1
  • VIPAS39
  • ZC4H2

Genes removed

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.