Genetic test

Lysosomal storage disorders - large panel

CAP & EMQN quality control

Price 2194 PLN 31 days from sample registration in laboratory 112 genes Sample Cheek swab or Venous blood or DNA

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What's included in the price

NGS sequencing — analysis of the full coding sequence
In-house result interpretation by our own team
Material collection / delivery per instructions
Result available online in the patient portal (PDF)

A consultation with a clinical geneticist is available as a separate service. See the clinic

About this test

Lysosomes are small follicles inside of which degradation of many substances takes place. Storage disorders result from defects in the enzymes present in lysosomes what leads to ineffective degradation and accumulation of substances inside the lysosomes. This may cause damage to cells and tissues.

Lysosomal disorders are a very broad group of almost 50 conditions. Despite the fact that each of the conditions is really rare lysosomal disorders as a group occurs in 1 in 7,000-8,000 people and may become apparent at any age. These starting in the infancy are more severe and affect the central nervous system, whereas the disorders with later onset tend to have much milder course and slower progression. Identification of the genetic change responsible for the disorders allows for more accurate prognosis.

Lysosomal disorders are inherited in an autosomal recessive pattern like Niemann-Pick disease or Gaucher disease, in which glucocerebrosidase deficiency leads to accumulation of cerebrosides and damage of internal organs such as liver, spleen, and bones. Some conditions, for example, Fabry disease and Hunter syndrome, have an X-linked pattern of inheritance. More and more therapies for lysosomal storage disorders are created based on the administration of deficient enzymes to the organism.

Genes analysed (112)

Gene	Inheritance	Associated condition
ABCC8	AD/AR	Diabetes mellitus, permanent neonatal 3, with or without neurologic features, Hyperinsulinemic hypoglycemia, familial, 3, Maturity-onset diabetes of the young, type 12
ACER1	—	—
ACER2	—	—
ACER3	—	—
ACY1	autosomal recessive	Aminoacylase 1 deficiency
ADSL	autosomal recessive	Adenylosuccinase deficiency
AGA	autosomal recessive	Aspartylglucosaminuria
ALDH5A1	autosomal recessive	Succinic semialdehyde dehydrogenase deficiency
ALDH7A1	autosomal recessive	Epilepsy, pyridoxine-dependent
AMT	autosomal recessive	Glycine encephalopathy
ANTXR2	autosomal recessive	—
AP5Z1	autosomal recessive	—
ARG1	autosomal recessive	Argininemia
ARSA	autosomal recessive	Metachromatic leukodystrophy
ARSB	autosomal recessive	—
ASAH1	autosomal recessive	Farber lipogranulomatosis, Spinal muscular atrophy with progressive myoclonic epilepsy
ASPA	autosomal recessive	Canavan disease, Canavan disease, Canavan disease
ATP13A2	autosomal recessive	Parkinson disease 19a, juvenile-onset
BTD	autosomal recessive	Biotinidase deficiencymultiple carboxylase deficiency, late-onset
CLN3	autosomal recessive	Ceroid lipofuscinosis, neuronal, 3, Ceroid lipofuscinosis, neuronal, 3
CLN5	autosomal recessive	Ceroid lipofuscinosis, neuronal, 5
CLN6	autosomal recessive	Ceroid lipofuscinosis, neuronal, 6
CLN8	autosomal recessive	Ceroid lipofuscinosis, neuronal, 8
COL11A2	AD/AR	Deafness, autosomal recessive 23, Fibrochondrogenesis 1, Otospondylomegaepiphyseal dysplasia, Otospondylomegaepiphyseal dysplasia, Stickler syndrome, type III
COL2A1	autosomal dominant	Avascular necrosis of femoral head, primary, 1, Epiphyseal dysplasia, multiple, with myopia and conductive deafness, Stickler syndrome, type I, Stickler syndrome, type III, Vitreoretinopathy with phalangeal epiphyseal dysplasia
CTNS	autosomal recessive	—
CTSA	autosomal recessive	—
CTSC	autosomal recessive	—
CTSD	autosomal recessive	Ceroid lipofuscinosis, neuronal, 10
CTSK	autosomal recessive	—
DHCR7	autosomal recessive	Smith-Lemli-Opitz syndrome
DPYD	AD/AR	—
DYM	autosomal recessive	Dyggve-Melchior-Clausen disease, Smith-Mccort dysplasia 1
ECM1	—	—
ETFA	autosomal recessive	Glutaricaciduria, type I, Multiple acyl-CoA dehydrogenation deficiency
ETFB	autosomal recessive	Glutaricaciduria, type I, Multiple acyl-CoA dehydrogenation deficiency
ETFDH	autosomal recessive	Glutaricaciduria, type I, Multiple acyl-CoA dehydrogenation deficiency
FH	autosomal dominant	Hereditary leiomyomatosis and renal cell cancer
FOLR1	autosomal recessive	Neurodegeneration due to cerebral folate transport deficiency
FUCA1	autosomal recessive	Fucosidosis
GAA	autosomal recessive	—
GALC	autosomal recessive	Krabbe disease, Krabbe disease
GALNS	autosomal recessive	—
GAMT	autosomal recessive	Cerebral creatine deficiency syndrome 2
GBA	autosomal recessive	Gaucher disease, type II
GCDH	autosomal recessive	Glutaricaciduria, type I
GLA	X-linked	Fabry disease
GLB1	autosomal recessive	GM1-gangliosidosis, type II, Mucopolysaccharidosis type IVB (Morquio)
GLDC	autosomal recessive	Glycine encephalopathy
GM2A	—	—
GNE	AD/AR	Nonaka myopathy
GNPTAB	autosomal recessive	Mucolipidosis IV
GNPTG	autosomal recessive	—
GNS	autosomal recessive	—
GPC3	X-linked	Simpson-Golabi-Behmel syndrome, type 1, Simpson-Golabi-Behmel syndrome, type 1
GUSB	autosomal recessive	Mucopolysaccharidosis VII
HEXA	autosomal recessive	Tay-Sachs disease
HEXB	autosomal recessive	Sandhoff disease
HGSNAT	autosomal recessive	—
HPD	AD/AR	—
HRAS	autosomal dominant	Bladder cancer, Bladder cancer, Congenital myopathy with excess of muscle spindles, Costello syndrome
HYAL1	autosomal recessive	—
IDS	X-linked	—
IDUA	autosomal recessive	—
L2HGDH	autosomal recessive	L-2-hydroxyglutaric aciduria
LAMA2	AD/AR	Muscular dystrophy, congenital, merosin deficient or partially deficient, Muscular dystrophy, limb-girdle, autosomal recessive 23
LAMP2	X-linked	Danon disease
LDB3	autosomal dominant	Cardiomyopathy, dilated, 1FF, Myopathy, myofibrillar, 1
LIPA	autosomal recessive	—
MAN1B1	autosomal recessive	—
MAN2B1	autosomal recessive	—
MANBA	autosomal recessive	Mannosidosis, beta
MCOLN1	autosomal recessive	Mucolipidosis IV
MFSD8	autosomal recessive	Ceroid lipofuscinosis, neuronal, 7
MOCS1	autosomal recessive	Molybdenum cofactor deficiency, complementation group A
MOCS2	autosomal recessive	—
MYOT	autosomal dominant	Myopathy, myofibrillar, 3
NAGA	autosomal recessive	—
NAGLU	autosomal recessive	—
NEU1	autosomal recessive	Neuraminidase deficiency
NPC1	autosomal recessive	—
NPC2	autosomal recessive	—
PEX1	autosomal recessive	—
PEX10	autosomal recessive	—
PEX12	autosomal recessive	—
PEX13	autosomal recessive	—
PEX16	autosomal recessive	—
PEX26	autosomal recessive	—
PEX3	autosomal recessive	—
PEX5	autosomal recessive	—
PEX6	autosomal recessive	Heimler syndrome 2
PGK1	X-linked	Phosphoglycerate kinase 1 deficiency
PHYH	autosomal recessive	—
PIGV	—	—
PPT1	autosomal recessive	Ceroid lipofuscinosis, neuronal, 1
PRODH	autosomal recessive	Hyperprolinemia, type I
PSAP	autosomal recessive	Gaucher disease, type II, Krabbe disease, Metachromatic leukodystrophy
QDPR	autosomal recessive	Dystonia, DOPA-responsive, with or without hyperphenylalaninemia
RAI1	autosomal dominant	—
RPS6KA3	X-linked	—
SGSH	autosomal recessive	—
SLC17A5	autosomal recessive	—
SLC25A15	autosomal recessive	Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome
SLC44A4	—	—
SLC46A1	autosomal recessive	Folate malabsorption, hereditary
SMPD1	autosomal recessive	Niemann-pick disease, type B
ST3GAL5	autosomal recessive	Salt and pepper developmental regression syndrome
SUMF1	autosomal recessive	Multiple sulfatase deficiency
SUOX	autosomal recessive	Sulfite oxidase deficiency
TCF4	autosomal dominant	ciężkie napady padaczkowe z dysfunkcją autonomicznego układu nerwowego, Pitt-Hopkins syndrome, Pitt-Hopkins syndrome
TPP1	autosomal recessive	Ceroid lipofuscinosis, neuronal, 2
VPS33A	—	—

Click a gene to see a single-gene test.

How the test works

1
Order online

No referral needed. You order online.
2
Collect the sample

Sample: Cheek swab or Venous blood or DNA.
3
Result

Available in 31 days from sample registration in laboratory, online.

Methodology

Information on the test method:

At first, deoxyribonucleic acid (DNA) is isolated from a blood sample or paraffin embedded tissue block. The quantity and quality of the material is determined in spectrophotometric and fluorometric assays. From mechanically or enzymatically fragmented DNA a library is made to be used for determination, sequencing and examination of selected genes. The library is sequenced on a new generation sequencer. Afterwards, sequencing results are subjected to bioinformatics analysis and clinical interpretation. Genetic variants are identified using BurrowsWheeler Aligner. The test detects 100% of substitutions and 95% of small insertions and deletions.

Information on variant classification:

The study report provides information on variants classified as ‘potentially pathogenic’ and ‘pathogenic’ depending on their suspected clinical significance. The identified variants are classified under the following categories:

Pathogenic variant: the detected change in the gene sequence directly associates with disease development. At the same time, some pathogenic changes may not have full penetration, meaning that a single mutation may not be enough to cause a full-blown disease.

Potentially pathogenic variant: the detected change in the gene sequence may be, with a great probability, associated with disease development however it is not possible to prove this association on the basis of currently available scientific data. Variant pathogenicity confirmation would require additional tests and evidence; it cannot be excluded that further tests might prove that the change has limited or no clinical significance.

Variant of unknown pathogenicity: based on the currently available scientific data it is not possible to determine the significance of the detected change.

Potentially benign variant: the detected change in the gene sequence most probably does not associate with disease development, however based on the currently available scientific data the benignity of the mutation cannot be confirmed. Confirmation of the clinical significance of the variant would require additional tests and evidence; it cannot be excluded that further tests might prove that the detected mutation has clinical significance and would cause disease development.

Benign variant: the detected change does not associate with disease development.

The identified genetic variants are classified based on the guidelines of the American College of Medical Genetics and Genomics and the American Association for Molecular Pathology (S. Richards, Genet Med. 2015 May; 17(5):405-24). In variant classification the following criteria are considered:

Previous variant identification in persons burdened with the disease
Variant impact of functional gene product synthesis determined through bioinformatics analyses, confirmed by in vitro/in vivo studies
Variant location (exon/intron, functional domain)
De novo/hereditary change
Variant incidence in general population (each variant with incidence >5% in line with Exome Sequencing Project, 1000 Genomes Project or Exome Aggregation Consortium is classified as benign change)

Variant incidence in general population with relation to patient population The final classification of variants is made on the basis of the total of the above-mentioned criteria. The data bases include: 1000GP, ClinVar, ConsensusPathDB, Exome Aggregation Consortium, Exome Variant Server, FATHMM, GO (Gene Ontology), GTEx (Genotype-Tissue Expression), GWAS (Genome Wide Association Study), HGMD, KEGG, MetaLR, MetaSVM, MutationAssessor, MutationTaster, OMIM, PolyPhen-2, PROVEAN, SIFT, SnpEff, dbNSFP, UniProt, VEP (Variant Effect Predictor).

Test limitations:

All sequencing technologies have some limitations. Our tests use new generation sequencing (NGS) to examine coding and splicing regions of disease-associated genes. Sequencing techniques and subsequent bioinformatics analyses are aimed at limiting the significance of pseudo-gene sequences, however presence of highly homologous gene sequences may still occasionally disturb the identification of pathogenic alleles, deletions/duplications. The Sanger sequencing method is used to confirm variants with lower quality parameters. Deletion/duplication analyses show qualitative changes in DNA covering at least one exon and always require confirmation with other methods (qPCR or MLPA). The analyses are not designed for detecting certain types of genomic changes, such as translocations, inversions, dynamic mutations (e.g. increased number of trinucleotide repetitions) or mutations in regulatory or intronic regions. In case increased numbers of di- or trinucleotide repetitions are reported, it should be assumed that the exact number of repetitions is not precise. The test is not intended to detect somatic mosaicism and somatic mutation analyses should be made in the context of the germinal DNA sequence.

It is not possible to exclude mutations in genes and regions other than those covered by the test as well as alternations in the gene copy number. The test report includes information on changes in gene sequence identified on the basis of a comparison against current reference sequences maintained in NCBI Nucleotide and Ensembl databases. Tests are developed by Warsaw Genomics for clinical objectives. All test results collected are interpreted and analysed by scientific and medical experts of Warsaw Genomics.

Frequently asked questions

How long does the Lysosomal storage disorders - large panel test take?

The result is usually available within 31 days from sample registration in laboratory.

Do I need a referral?

No. You can order this genetic test online without a referral.

How many genes does this panel cover?

The panel analyses 112 genes.

How much does the test cost?

The price of the test is 2194 PLN.

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Test price

2194 PLN