1. NGS panel - Genetic testing for Mucopolysaccharidosis

Mucopolysaccharidosis

July 17, 2017

Clinical features

Mucopolysaccharidoses are a group of rare inherited metabolic disorders caused by the absence or dysfunction of lysosomal enzymes and subsequent lysosomal storage of glycosaminoglycans. This group of numerous and highly diverse diseases, with a broad range of symptoms and genetic causes, can be classified in several different subtypes (Table).


Classification of mucopolysaccharidosis and an overview of associated genes

MPS subtype MPS name MPS gene MPS locus Protein/Enzyme Incidence
MPS I Hurler, Hurler-Scheie, Scheie IDUA 4p16.3 α-duronidase 1/100,000
MPS II Hunter IDS Xq28 Iduronate sulfatase 1/140,000
MPS III A Sanfilippo A SGSH 17q25.3 Heparan-N-sulfatase 1/70,000-90,000
MPS III B Sanfilippo B NAGLU 17q21.1 α-N-acetylglucosaminidase 1/70,000-90,000
MPS III C Sanfilippo C HGSNAT 14p21 AcetylCoA α-glucosamine acetyltransferase 1/70,000-90,000
MPS III D Sanfilippo D GNS 12q14 N-acetylglucosamine 6-sulfatase 1/70,000-90,000
MPS IV A Morquio A 1GALNS 16q24.3 Galactosamine-6-sulfate sulfatase 1/200,000
MPS IV B Morquio B GLB1 3p21.3 >α-galactosidase 1/200,000
MPS VI Maroteaus-Lamy ARSB 5q11–q13 N-acetylgalactamine 4-sulfatase 1/240,000-300,000
MPS VII Sly GUSB 7q21.11 α-glucuronidase <1/250,000
MPS IX Natowicz HYAL1 3p21.3 Hyaluronidase 1 Very rare

Mucopolysaccharidosis type I (MPS I, Hurler syndrome, Scheie syndrome, Hurler-scheie syndrome) is a progressive multisystemic lysosomal disease caused by a deficiency of α-iduronidase (IDUA). MPS I is inherited in an autosomal recessive manner and has an incidence of approximately 1 in 100,000 live births for the Hurler phenotype 1, 2 and up to 1 in 500,000 live births for the Scheie phenotype 1, 3. The most common clinical manifestations of MPS I include the following:

  • Characteristic coarse facial features
  • Frequent upper-respiratory infections and otitis media
  • Hepatosplenomegaly
  • Inguinal or umbilical hernia
  • Characteristic skeletal and joint findings
  • Characteristic ocular findings (corneal clouding).

MPS I is commonly classified into severe and attenuated forms, i.e. three highly variable and overlapping clinical syndromes: Hurler, Hurler-Scheie, and Scheie 4. Hurler syndrome is a severe subtype of MPS I, characterized by early onset (~9 months of age) and multiple organ involvement. Hurler-Scheie and Scheie syndromes are attenuated forms of MPS I, with onset at 24 months of age or later, and with less severe features than Hurler syndrome 4.

Mucopolysaccharidosis type I is caused by mutations in the IDUA gene which encodes enzyme alpha-L-iduronidase (IDUA). IDUA is a glycosidase that removes non-reducing terminal α-L-iduronide residues during the lysosomal degradation and mutations in IDUA result in its loss of function and the accumulation of partially degraded glycosaminoglycans (GAGs). The Human Gene Mutation database (HGMD® Professional 2017.1) currently lists more than 250 IDUA pathogenic variants associated with MPS I. Known IDUA pathogenic variants include nonsense, missense, and splice site variants, small deletions, and insertions. The most common IDUA pathogenic variants are p.Gln70Ter and p.Trp402Ter:

  • The pathogenic variant p.Gln70Ter was observed in 35% of MPS I-patients of European origin 5, in 19% of patients in Netherlands and Germany 4, in 65% of patients in Scandinavia 5, 68% patients in Russia 6, and 17% in North American population 7
  • The pathogenic variant p.Trp402Ter was identified in 37% of European 5, 48% of patients in Netherlands and German 4, 43% of North American 7 and 55% of Australasian patients 4.

In addition, the mutations most common for MPS I-affected patients in Japan are p.Arg89Gln (24%) and c.613_617dupTGCTC 3 (18%) 8. Common IDUA mutations detected in the Italian population include p.Pro533Arg (11%), p.Gly51Asp (9.3%) and p.Ala327Pro (5.6%) 9. The mutation p.Arg619* was found at a high frequency in 25% of MPS I patients in the Indian population 10. The most common IDUA mutation found at a frequency of 42.8% was W402X in Colombia, Ecuador, and Peru 11.

Mucopolysaccharidosis II (Hunter syndrome) is a rare X-linked genetic disease characterized by glycosaminoglycan (GAG) accumulation and is caused by a deficiency of the lysosomal enzyme iduronate-2-sulfatase (IDS). MPS II has an incidence between 1/100,000 and 1/170,000 male births 12, 13, 14. MPS II is found almost exclusively in young males and is clinically characterized by short stature, hepatosplenomegaly, joint contractures, and coarse facies. Early signs and symptoms of MPS II include ear/sinus infections and umbilical hernia, behavioral disturbance, and skeletal anomalies. However, for the diagnosis of MPS II IDS enzyme activity tests are necessary and molecular genetic test for IDS mutations are critical.

More than 600 IDS pathogenic variants have been described. Single-nucleotide changes and splicing mutations account for 65% of all pathogenic variants; small deletions and insertions account for 17% of all pathogenic variants. Lack of genotype/phenotype correlation is demonstrated by identification of several missense pathogenic variants, including the following: p.Arg468Gln, p.Arg468Trp, and p.Ser333Leu. These IDS variants were identified in individuals with the early progressive phenotype and others with the intermediate or slowly progressive phenotype 15. Furthermore, a 178-bp deletion in the promoter region of IDS was identified in affected individuals with low IDS enzyme activity 16. Alteration of the promoter region may explain low enzyme activity in some affected individuals in whom no IDS pathogenic variant in the coding region or deletion of exon/exons or the whole gene were detected.

Mucopolysaccharidosis type III (MPS III), also known as Sanfilippo syndrome, is a lysosomal storage disorder, caused by a deficiency in one of the four enzymes involved in the catabolism of glycosaminoglycan heparan sulfate encoded by genes GNS, HGSNAT, NAGLU, and SGSH. MPS III is characterized by progressive cognitive decline and severe hyperactivity, with relatively mild somatic features. The estimated incidence of all four MPS III types combined is 1 in 70,000 newborns 17, 18. MPS IIIA and MPS IIIB are much more common than MPS IIIC and MPS IIID.

The major features of MPS III include the following:

  • Onset of symptoms is usually between 2 and 6 years
  • Presenting symptoms include hyperactive, aggressive and destructive behaviors and sleep disturbances
  • Mental development abnormalities starts slowly and progresses to severe dysfunctions of gait and speech. By age 10 years patients are severely limited in their activities and movement.
  • Most children with MPS type IIIA have severe neurological impairment by age 6 years
  • Recurrent or chronic diarrhea and seizures occurs in some MPS III patients. Respiratory complications could occur and upper respiratory tract infections and sinopulmonary disease are common.

Unfortunately, there is currently no cure or standard treatment for people with Mucopolysaccharidosis type IIIA (MPS IIIA). Affected people and their families should consult a medical genetics team for information about the diagnosis, counseling, up-to-date treatment options, and referrals to support groups and organizations. Treatment requires ongoing care with trained pediatric specialists in various medical fields. A consultation with a developmental pediatrician is especially helpful in addressing behavioral concerns and to assist parents and caregivers in establishing a sleep routine.

Mucopolysaccharidosis type IIIA (MPS3A) is caused by homozygous or compound heterozygous mutations in the gene encoding N-sulfoglucosamine sulfohydrolase (SGSH). Specific SGSH mutations have been found in high frequencies in distinct geographical locations:

  • The missense mutation p.R74C occurs at a frequency of 56% of the Polish population 19
  • The p.R245H variant is found in 31% of mutant alleles in Australia, 35% of those in Germany, and 58% of those in Netherlands 20, 21
  • The p.S66W missense mutation is found in 29% of alleles in a cohort of Italian patients 22

Mucopolysaccharidosis type IIIB or Sanfilippo syndrome B is caused by homozygous or compound heterozygous mutation in the gene encoding N-alpha-acetylglucosaminidase (NAGLU). Most of the known mutations in MPS IIIB patients are not common and occur at low frequencies. However, the p.F48L, p.G69S, p.S612G, and p.R643C missense mutations have been associated with a later-onset phenotype 23. Several NAGLU mutations have been reported with Charcot-Marie-Tooth disease, axonal, type 2V.

Mucopolysaccharidosis type IIIC (MPS3C), also known as Sanfilippo syndrome C, is caused by homozygous or compound heterozygous mutation in the HGSNAT gene (610453), encoding heparan acetyl-CoA:alpha-glucosaminide N-acetyltransferase, on chromosome 8p11.

The missense mutations p.R344C and p.S518F account for 22% and 29%, respectively, of mutant alleles in Netherlands 24.

Furthermore, the deleterious nature of nearly all known missense mutations can be established via their occurrence in amino acids present in a transmembrane domain and/or conservation among orthologs 25, 26. Interestingly, mutations in HGSNAT have been found in six patients with the non-syndromic form of retinitis pigmentosa, each of whom was diagnosed in their third to fifth decade of life 27.

Mucopolysaccharidosis type IIID (MPS3D) is caused by homozygous mutations in the gene encoding N-acetylglucosamine-6-sulfatase (GNS). Similar to MPS IIIB, there are no common mutations in MPS IIID and there are relatively few missense mutations compared with the other subtypes of MPS III (~13%) 18, and the dominant mutations are deletions, insertions, and rearrangements.

Mucopolysaccharidosis type IV (MPS IV), also known as Morquio syndrome is a rare progressive lysosomal storage disease characterized by skeletal abnormalities. The exact prevalence of MPS IV is unknown, although it is estimated to occur in 1 in 200,000 to 300,000 individuals. The birth prevalence for MPS IVA ranged from 1:71,000 to 1:179,000 across multiple countries 28.

Mucopolysaccharidosis IVA should be suspected in an individual with the following findings 29:

  • Marked disproportionate short stature with short trunk and normal limbs
  • Respiratory complications (sleep apnea, endurance limitations, snoring)
  • Cardiac valve abnormalities
  • Dental abnormalities
  • Pectus carinatum, kyphosis, scoliosis, genu valgum, hypermobile joints
  • Waddling gait with frequent falls
  • Qualitative urine glycosaminoglycan (GAG) analysis demonstrates keratan sulfate and chondroitin 6-sulfate.

Mucopolysaccharidosis type IVA is caused by homozygous or compound heterozygous mutations in the GALNS gene. Missense, nonsense, and splicing variants, as well as small deletions, small insertions, gross insertions/duplications, and gross deletions have been found in GALNS. Approximately 26% of pathogenic missense variants were caused by transitional mutations at CpG dinucleotides, the role of methylation in regulation of GALNS was identified: methylation was extensive within exons 2 through 30.

Mucopolysaccharidosis type IVB (Morquio syndrome B) is caused by mutations in the gene encoding beta-galactosidase (GLB1). Morquio syndrome B is allelic to the various forms of GM1-gangliosidosis. GM1 gangliosidosis includes phenotypes that range from severe to mild. MPS IVB is characterized by skeletal changes, including short stature and skeletal dysplasia. More than 200 mutations have been reported in the GLB1 gene, the majority of which are missense mutations (>80%) and small insertions/deletions. The frequencies of mutations p.R59H and 1622-1627insG in the GLB1 gene among the South American patients were 19.2% and 38.5%, respectively 31. The overall frequency of either p.R59H or 1622-1627insG was 57.7% of the disease-causing alleles, and this epidemiological study suggested a carrier frequency of 1:58 for this population 31. The most common GLB1 mutation in the Gypsy population is p.R59H 32.

Mucopolysaccharidosis VI (MPS VI) is a rare lysosomal storage disease associated with a deficiency of arylsulfatase B. The disorder shows a wide spectrum of symptoms from slowly to rapidly progressing forms. The characteristic skeletal dysplasia includes short stature, dysostosis multiplex, and degenerative joint disease. Birth prevalence is between 1 in 43,261 and 1 in 1,505,160 live births 33.

MPS VI is transmitted in an autosomal recessive manner and is caused by mutations in the ARSB gene, located in chromosome 5 (5q13-5q14). Over 190 ARSB mutations have been reported, causing absent or reduced arylsulfatase B (N-acetylgalactosamine 4-sulfatase) activity and interrupted dermatan sulfate and chondroitin sulfate degradation.

Mucopolysaccharidosis type VII (MPS VII, Sly syndrome), is a progressive multisystem lysosomal storage disease characterized by a wide variety of symptoms. The most severe form is characterized by hydrops fetalis and premature or very early death. Other forms of MPS VII are less severe and present during early childhood and are characterized by the following signs and symptoms:

  • Macrocephaly and hydrocephalus
  • Distinctive facial features and macroglossia
  • Hepatosplenomegaly
  • Cardiac valve abnormalities
  • Umbilical and/or inguinal hernia
  • Frequent upper respiratory infections, otitis media, hearing loss
  • Sleep apnea
  • Cloudy corneas and vision loss.

MPS VII is one of the rarest types of Mucopolysaccharidosis with the estimated prevalence of 1 in 250,000 newborns 34. It is caused by homozygous or compound heterozygous mutations in the gene encoding beta-glucuronidase (GUSB) on chromosome 7q11. More than 60 mutations have been reported in GUSB, majority of them missense and only few small deletions and splice mutations.

Mucopolysaccharidosis type IX is a very rare lysosomal storage disease reported in only few patients so far. It is characterized by mild clinical phenotype, including mild short stature, an absence of neurological or visceral involvement, and histological and ultrastructural evidence of a lysosomal storage disease. MPS IX is caused by compound heterozygous mutation in the HYAL1 gene on chromosome 3p21. Only 2 pathogenic variants have been reported for the HYAL1 gene:

  • Missense mutation c.802G>A; p.E268K reported in association with short stature phenotype 35
  • Small deletion c.104delT reported in a single consanguineous family with three affected children presenting with knee and/or hip pain associated with swelling 36

Therapeutic options for Mucopolysaccharidosis:

Mucopolysaccharidosis type I: treatment should include learning programs and special education for developmental delays, cardiac valve replacement as needed; physical therapy, orthopedic surgery, and other treatments.

Mucopolysaccharidosis type II: Interventions for MPS II commonly include occupational and physical therapy; shunting for hydrocephalus; tonsillectomy and adenoidectomy and others. Enzyme replacement therapy (ERT) with idursulfase (Elaprase®), a recombinant form of human iduronate 2-sulfatase, was approved in the United States and the European Union in individuals with the slowly progressing form of the disease 12.

Mucopolysaccharidosis type III, VII, IX: Medical treatment is supportive and is directed toward improving the patient's quality of life.

Mucopolysaccharidosis type VI: Enzyme replacement therapy with galsulfase (Naglazyme) has been shown to improve walking and stair-climbing capacity and to decrease urine glycosaminoglycan (GAG) levels in patients with MPS VI 37.

CENTOGENE offers full gene sequencing and deletion/duplication analysis for the Mucopolysaccharidosis panel (genes: ARSB, GALNS, GLB1, GNPTAB, GNPTG, GNS, GUSB, HGSNAT, IDS, IDUA, NAGLU, SGSH).


Differential diagnosis

The differential diagnosis of Mucopolysaccharidosis-related disorders – depending on the major symptoms in the initial case – includes the following diseases:

Mucopolysaccharidosis I:

  • Lysosomal storage disease (MPS II, MPS IVA, multiple sulfatase deficiency, mucolipidosis I, mucolipidosis II, mucolipidosis III alpha/beta, and alpha-mannosidosis)
  • Juvenile idiopathic arthritis

Mucopolysaccharidosis II:

  • Other subtypes of MPS
  • Multiple sulfatase deficiency
  • Mucolipidosis types II and III

Mucopolysaccharidosis III, VI, VII, IX:

  • Other subtypes of MPS
  • Multiple sulfatase deficiency (Austin disease)

Testing strategy

CENTOGENE offers an advanced, fast and cost-effective strategy to test large NGS panels and diagnose complex phenotypes based on PCR-free whole genome sequencing and NGS technology. This approach offers an unparalleled advantage by reducing amplification/capture biases and providing sequencing of the entire gene with more uniform coverage.

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for Mucopolysaccharidosis panel using NGS Panel Genomic targeted towards this specific phenotype:

Step 1: Whole genome sequencing from a single filter card. The sequencing covers the entire genic region (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the Mucopolysaccharidosis panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no mutation is identified after analysis of the Mucopolysaccharidosis panel, we recommend continuing the bioinformatics analysis of the data obtained through whole genome sequencing to cover those genes which are either implicated in an overlapping phenotype or could be involved in a similar pathway but are not strongly clinically implicated based on the current information in literature.


Referral reasons

The following individuals are candidates for mucopolysaccharidosis testing:

  • Individuals with a family history of mucopolysaccharidosis and presentation of the most common symptoms
  • Individuals without a positive family history, but with symptoms resembling mucopolysaccharidosis
  • Individuals with a negative but suspected family history of mucopolysaccharidosis, in order to perform proper genetic counseling.

Test utility

Sequencing, deletion/duplication of the panel genes should be performed in all individuals suspected of having mucopolysaccharidosis and suspected phenotypes. In parallel, other genes reported to be related with this clinical phenotype should also be analyzed for the presence of mutations, due to the overlap in many clinical features caused by those particular genes.

Confirmation of a clinical diagnosis through genetic testing can allow for genetic counseling and may direct medical management. Genetic counseling can provide a patient and/or family with the natural history of the mucopolysaccharidosis and related disorders identify at-risk family members, provide disease risks as well as appropriate referral for patient support and/or resources.


More information on CENTOGENE´s Mucopolysaccharidosis panel can be found in our genetic test catalogue.