Alternative titles; symbols
HGNC Approved Gene Symbol: DPAGT1
SNOMEDCT: 725079003;
Cytogenetic location: 11q23.3 Genomic coordinates (GRCh38) : 11:119,093,874-119,101,853 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 11q23.3 | Congenital disorder of glycosylation, type Ij | 608093 | Autosomal recessive | 3 |
| Myasthenic syndrome, congenital, 13, with tubular aggregates | 614750 | Autosomal recessive | 3 |
N-linked glycosylation is initiated in all eukaryotic cells with the synthesis of lipid-linked oligosaccharides in a cyclic pathway, the dolichol cycle. DPAGT1 (EC 2.7.8.15) catalyzes the first step in the dolichol cycle, the synthesis of N-acetylglucosaminyl-pyrophosphoryldolichol (GlcNAc-PP-dolichol) from dolichol phosphate and UDP-GlcNAc, and can be inhibited by the antibiotic tunicamycin (Eckert et al., 1998).
Rajput et al. (1992) isolated mRNA for the Dpagt1 protein from mouse mammary glands. The mouse cDNA recognized a single mRNA species of about 2 kb in mouse mammary glands when used as a probe in Northern blot analysis.
Eckert et al. (1998) cloned a human DPAGT1 cDNA from a human lung fibroblast cDNA library. The cDNA encodes a deduced 400-amino acid protein with a calculated molecular mass of 44.7 kD. DPAGT1 contains an N-terminal signal peptide, 2 potential dolichol-binding sequences, and 4 sites for N-glycosylation. It shares 93% amino acid homology with hamster Dpagt, including 100% identity in the dolichol-binding region, and 42% homology with S. cerevisiae GlcNAc-1-P transferase.
Protein asparagine-linked glycosylation is a multistep process that is divided into 2 stages. The first stage consists of the synthesis of the lipid-linked oligosaccharide precursor (LLO) and its en bloc transfer to nascent polypeptides in the lumen of the endoplasmic reticulum. This process requires at least 34 genes, of which DPAGT1 is the first. The second stage involves the processing of protein-bound oligosaccharides and requires at least an additional 20 genes to form a bi-antennary sugar chain typical of plasma glycoproteins. Genetic defects in some of these genes, including DPAGT1, cause severe multisystem disorders called congenital disorders of glycosylation (CDGs) (Freeze, 2001)
Eckert et al. (1998) demonstrated that S. cerevisiae expressing recombinant DPAGT1 synthesized GlcNAc- and GlcNAc(2)-PP-dolichol. Expression of human DPAGT1 also complemented a conditional lethal S. cerevisiae strain defective for GlcNAc-1-P transferase. Expression of recombinant DPAGT1 from a multicopy expression vector also conferred a higher tolerance toward tunicamycin due to elevated enzyme synthesis, thus showing a gene dosage effect.
Dong et al. (2018) determined the crystal structures of human DPAGT1 and DPAGT1 in complex with UDP-GlcNAc or tunicamycin at 3.1- to 3.6-angstrom resolution. DPAGT1 exists predominantly as a noncovalent dimer in solution, and dimerization is important for its stability. DPAGT1 consists of 10 transmembrane helices (TMHs) with both termini in the endoplasmic reticulum (ER) lumen. The active site is on the cytoplasmic face of the membrane, formed by 4 of the 5 cytoplasmic loops between the TMHs. Three loops are on the ER side of the membrane, and 1 is embedded in the membrane on the ER side. Formation of the DPAGT1-UDP-GlcNAc complex stabilizes the active site of DPAGT1. The authors determined that missense mutations in DPAGT1 alter DPAGT1 function via diverse mechanisms. Structural analysis of the DPAGT1-tunicamycin complex suggested that tunicamycin inhibits DPAGT1 through partial mimicry of the complex formed during catalysis between acceptor phospholipid Dol-P and UDP-GlcNAc. The authors designed semisynthetic and lipid-altered tunicamycin analogs that retained antimicrobial activity but no longer inhibited DPAGT1, thereby circumventing toxicity to eukaryotic cells. These tunicamycin analogs could reduce intracellular bacterial burdens with nanomolar antimicrobial potency and no signs of toxicity, providing leads for tuberculosis antibiotic development.
Using FISH and somatic cell hybrid analysis, Smith et al. (1993) mapped the DPAGT1 gene (D11S366) to chromosome 11q23.3.
Using a panel of mouse/hamster somatic cell hybrids and a specific probe derived from the 3-prime noncoding region of the mouse cDNA, Rajput et al. (1992) mapped the mouse Dpagt1 gene to chromosome 17.
Marek et al. (1999) found that Dpagt1-null mice died 4 to 5 days postfertilization, just after implantation, suggesting that DPAGT1 function and protein N-glycosylation are essential in early embryogenesis.
Congenital Disorder of Glycosylation Type Ij
In a patient with CDG Ij (CDGIJ; 608093), Wu et al. (2003) identified a tyr170-to-cys mutation (Y170C; 191350.0001) in the DPAGT1 gene.
Timal et al. (2012) identified compound heterozygosity for 2 mutations in the DPAGT1 gene (191350.0007 and 191350.0008) in a Caucasian boy with CDG Ij. The mutations were found by exome sequencing and confirmed by Sanger sequencing.
In 2 sibs, born of consanguineous Turkish parents, with severe CDG Ij, Wurde et al. (2012) identified a homozygous mutation in the DPAGT1 gene (A114G; 191350.0009). The mutation was found by homozygosity mapping followed by candidate gene sequencing. The unaffected parents were heterozygous for the mutation, which was not found in 100 control alleles of the same ethnic background. RT-PCR analysis of patient cells showed that the mutation also increased the amount of normal aberrant splicing seen in controls, resulting in the skipping of exons 2/3 and a truncated protein. In vitro functional expression assays showed decreased DPAGT1 activity, at 18% of normal values. The patients had a severe disorder characterized by hyperexcitability, intractable seizures, bilateral cataracts, nystagmus, strabismus, and progressive microcephaly. Both died within their first year of life from cardiorespiratory failure.
In a Pakistani brother and sister, born of unrelated patients with a mild from of CDG Ij, Iqbal et al. (2013) identified compound heterozygous mutations in the DPAGT1 gene (I29F; 191350.0010 and L168P; 191350.0011). The mutations were found by exome sequencing, confirmed by Sanger sequencing, segregated with the disorder, and occurred at highly conserved residues. Neither was present in over 200 ethnically matched chromosomes or in the dbSNP, 1000 Genomes Project, or Exome Variant Server databases. Functional studies of the variants were not performed. The patients had normal psychomotor development until ages 2 and 5 years, respectively, when they both developed seizures, hypotonia, and aggressive behavior. As adults, they had moderate intellectual disability, poor speech, aggressive behavior, hypotonia, seizures, and mild facial dysmorphic features.
Congenital Myasthenic Syndrome 13
In 5 patients from 4 families with congenital myasthenic syndrome-13 (CMS13; 614750) with tubular aggregates, Belaya et al. (2012) identified 7 different mutations in the DPAGT1 gene (see, e.g., 191350.0002-191350.0006). All mutations were in the compound heterozygous state. The first 4 mutations were identified by exome sequencing of 2 unrelated patients and were confirmed by Sanger sequencing. The mutations segregated with the disorder in those families with available material. Analyses of motor endplates from 2 patients showed a severe reduction of endplate acetylcholine receptors (AChR). In vitro studies showed that DPAGT1 is required for efficient glycosylation of AChR subunits and for efficient export of AChR receptors to the cell surface. The findings demonstrated the importance of N-linked protein glycosylation for proper functioning of the neuromuscular junction, and suggested that the primary pathogenic mechanism of DPAGT1 mutations is reduced levels of AChR at the endplate region. Laboratory studies of 2 patients showed abnormal glycosylation of transferrin, consistent with a functional defect of DPAGT1. Belaya et al. (2012) postulated that the defect in glycosylation of certain proteins may lead to misfolding and aggregation in the sarcoplasmic reticulum, resulting in formation of tubular aggregates within muscle tissue.
GPT has been used as an abbreviation for this enzyme, but this runs the risk of confusion with glutamate-pyruvate transaminase (GPT; 138200).
In a patient with central disorder of glycosylation type Ij (CDG1J; 608093), Wu et al. (2003) identified reduced DPAGT1 enzymatic activity; sequencing of genomic DNA and cDNAs of the DPAGT1 gene identified, in the paternal allele, a 660A-G transition in exon 5, resulting in a tyr170-to-cys (Y170C) mutation. Although no mutation was identified in the maternal allele, it produced only 12% of the normal amount of mature mRNA; the remainder showed a complex exon skipping pattern that shifted the reading frame and resulted in a truncated nonfunctional protein. The patient had developed infantile spasms at the age of 4 months within 72 hours of receiving DPT immunization. Development was significantly delayed in all aspects with microcephaly, arched palate, micrognathia, and exotropia. She also had fifth finger clinodactyly, single flexion creases of the hands, and skin dimples on the upper thighs. She had severe hypotonia and medically intractable seizures, and at 6 years of age had minimal speech. Abnormal isoelectric focusing pattern of serum transferrin was consistent with the diagnosis of type I CDG.
In a patient with congenital myasthenic syndrome-13 (CMS13; 614750), Belaya et al. (2012) identified compound heterozygosity for 2 mutations in the DPAGT1 gene: a 349G-A transition resulting in a val117-to-ile (V117I) substitution, and a 324G-C transversion resulting in a met108-to-ile (M108I; 191350.0003) substitution. Another patient was compound heterozygous for V117I and a 1-bp duplication (c.699dup; 191350.0004), resulting in a frameshift, premature termination (Thr234HisfsTer116), and nonsense-mediated mRNA decay. The mutations were found by exome sequencing and confirmed by Sanger sequencing. The 324G-C mutation was found in 2 (0.0186%) of 10,758 control alleles from the general population and 1 (0.0142%) of 7,020 alleles in the European American population. None of the other mutations were found in controls. The patients had onset at age 2.5 and 7 years, respectively, of difficulty walking due to proximal muscle weakness, and showed a favorable response to pyridostigmine. Muscle biopsy showed reduced levels of endplate acetylcholine receptors (AChR). In vitro functional expression studies showed that the c.699dup mutation was unable to restore normal levels of glycosylated AChR in HEK293 cells with DPAGT1 inhibition.
For discussion of the met108-to-ile (M108I) mutation in the DPAGT1 gene that was found in compound heterozygous state in a patient with congenital myasthenic syndrome-13 (CMS13; 614750) by Belaya et al. (2012), see 191350.0002.
For discussion of the 1-bp duplication in the DPAGT1 gene (699dup) that was found in compound heterozygous state in a patient with congenital myasthenic syndrome-13 (CMS13; 614750) by Belaya et al. (2012), see 191350.0002.
In 2 sibs with congenital myasthenic syndrome-13 (CMS13; 614750), Belaya et al. (2012) identified compound heterozygosity for 2 mutations in the DPAGT1 gene: a 358C-A transversion resulting in a leu120-to-met (L120M) substitution, and a 791T-G transversion resulting in a val264-to-gly (V264G; 191350.0006) substitution. The patients had onset in the first year of life of hypotonia, poor head control, and delayed motor development. They showed some improvement in muscle power during the teenage years, and both showed a response to pyridostigmine.
For discussion of the val264-to-gly (V264G) mutation in the DPAGT1 gene that was found in compound heterozygous state in patients with congenital myasthenic syndrome-13 (CMS13; 614750) by Belaya et al. (2012), see 191350.0005.
In a patient with congenital disorder of glycosylation type Ij (CDGIJ; 608093), Timal et al. (2012) identified compound heterozygosity for 2 mutations in the DPAGT1 gene: a 206T-A transversion in exon 2 resulting in an ile69-to-asn (I69N) substitution at a highly conserved residue in the highly conserved dolichol recognition motif, and a G-to-A transition in intron 1 (161+5G-A; 191350.0008), which resulted in degradation of the mutant mRNA. The mutations were found by exome sequencing and confirmed by Sanger sequencing. Each unaffected parent was heterozygous for 1 of the mutations. In patient-derived cells, the formation of GlcNAc-PP-dolichol was reduced to 22% of controls. The patient had multisystem problems, including asphyxia at birth, respiratory insufficiency, frequent apneas, jaundice, nuclear cataracts, cryptorchidism, dysmorphic features, hypertonia of the limbs, joint contractures, tremor, and feeding difficulties. Laboratory studies showed chronic anemia, hypoproteinemia, increased liver enzymes, and coagulation defects.
For discussion of the splice site mutation in the DPAGT1 gene (161+5G-A) that was found in compound heterozygous state in a patient with congenital disorder of glycosylation type Ij (CDGIJ; 608093) by Timal et al. (2012), see 191350.0007.
In 2 sibs, born of consanguineous Turkish parents, with congenital disorder of glycosylation type Ij (CDGIJ; 608093), Wurde et al. (2012) identified a homozygous c.341C-G transversion in exon 3 of the DPAGT1 gene, resulting in an ala114-to-gly (A114G) substitution. The mutation was found by homozygosity mapping followed by candidate gene sequencing. The unaffected parents were heterozygous for the mutation, which was not found in 100 control alleles of the same ethnic background. RT-PCR of patient cells showed that the mutation also increased the normal aberrant splicing seen in controls, resulting in the skipping of exons 2/3 and a truncated protein. In vitro functional expression assays showed decreased DPAGT1 activity, at 18% of normal values. The patients had a severe disorder characterized by hyperexcitability, intractable seizures, bilateral cataracts, nystagmus, strabismus, and progressive microcephaly. Both died within their first year of life from cardiorespiratory failure.
In 2 Pakistani sibs, born of unrelated parents, with a relatively mild form of congenital disorder of glycosylation type Ij (CDGIJ; 608093), Iqbal et al. (2013) identified compound heterozygosity for 2 mutations in the DPAGT1 gene: a c.85A-T transition resulting in an ile29-to-phe (I29F) substitution, and a c.503T-C transition resulting in a leu168-to-pro (L168P; 191350.0011) substitution. The mutations were found by exome sequencing of 1 of the patients and confirmed by Sanger sequencing in both patients. The mutations segregated with the disorder and occurred at highly conserved residues. Neither was present in over 200 ethnically matched chromosomes or in the dbSNP, 1000 Genomes Project, or Exome Variant Server databases. Functional studies of the variants were not performed.
For discussion of the leu168-to-pro (L168P) mutation in the DPAGT1 gene that was found in compound heterozygous state in patients with congenital disorder of glycosylation type Ij (CDGIJ; 608093) by Iqbal et al. (2013), see 191350.0010.
Belaya, K., Finlayson, S., Slater, C. R., Cossins, J., Liu, W. W., Maxwell, S., McGowan, S. J., Maslau, S., Twigg, S. R. F., Walls, T. J., Pascual Pascual, S. I., Palace, J., Beeson, D. Mutations in DPAGT1 cause a limb-girdle congenital myasthenic syndrome with tubular aggregates. Am. J. Hum. Genet. 91: 193-201, 2012. [PubMed: 22742743] [Full Text: https://doi.org/10.1016/j.ajhg.2012.05.022]
Dong, Y. Y., Wang, H., Pike, A. C. W., Cochrane, S. A., Hamedzadeh, S., Wyszynski, F. J., Bushell, S. R., Royer, S. F., Widdick, D. A., Sajid, A., Boshoff, H. I., Park, Y., and 20 others. Structures of DPAGT1 explain glycosylation disease mechanisms and advance TB antibiotic design. Cell 175: 1045-1058, 2018. [PubMed: 30388443] [Full Text: https://doi.org/10.1016/j.cell.2018.10.037]
Eckert, V., Blank, M., Mazhari-Tabrizi, R., Mumberg, D., Funk, M., Schwarz, R. T. Cloning and functional expression of the human GlcNAc-1-P transferase, the enzyme for the committed step of the dolichol cycle, by heterologous complementation in Saccharomyces cerevisiae. Glycobiology 8: 77-85, 1998. [PubMed: 9451016] [Full Text: https://doi.org/10.1093/glycob/8.1.77]
Freeze, H. H. Update and perspectives on congenital disorders of glycosylation. Glycobiology 11: 129R-143R, 2001. [PubMed: 11805072]
Iqbal, Z., Shahzad, M., Vissers, L. E. L. M., van Scherpenzeel, M., Gilissen, C., Razzaq, A., Zahoor, M. Y., Khan, S. N., Kleefstra, T., Veltman, J. A., de Brouwer, A. P. M., Lefeber, D. J., van Bokhoven, H., Riazuddin, S. A compound heterozygous mutation in DPAGT1 results in a congenital disorder of glycosylation with a relatively mild phenotype. Europ. J. Hum. Genet. 21: 844-849, 2013. [PubMed: 23249953] [Full Text: https://doi.org/10.1038/ejhg.2012.257]
Marek, K. W., Vijay, I. K., Marth, J. D. A recessive deletion in the GlcNAc-1-phosphotransferase gene results in peri-implantation embryonic lethality. Glycobiology 9: 1263-1271, 1999. [PubMed: 10536042] [Full Text: https://doi.org/10.1093/glycob/9.11.1263]
Rajput, B., Ma, J., Muniappa, N., Schantz, L., Naylor, S. L., Lalley, P. A., Vijay, I. K. Mouse UDP-GlcNAc:dolichyl-phosphate N-acetylglucosaminephosphotransferase: molecular cloning of the cDNA, generation of anti-peptide antibodies and chromosomal localization. Biochem. J. 285: 985-992, 1992. [PubMed: 1323278] [Full Text: https://doi.org/10.1042/bj2850985]
Smith, M. W., Clark, S. P., Hutchinson, J. S., Wei, Y. H., Churukian, A. C., Daniels, L. B., Diggle, K. L., Gen, M. W., Romo, A. J., Lin, Y., Selleri, L., Mcelligott, D. L., Evans, G. A. A sequence-tagged site map of human chromosome 11. Genomics 17: 699-725, 1993. [PubMed: 8244387] [Full Text: https://doi.org/10.1006/geno.1993.1392]
Timal, S., Hoischen, A., Lehle, L., Adamowicz, M., Huijben, K., Sykut-Cegielska, J., Paprocka, J., Jamroz, E., van Spronsen, F. J., Korner, C., Gilissen, C., Rodenburg, R. J., Eidhof, I., Van den Heuvel, L., Thiel, C., Wevers, R. A., Morava, E., Veltman, J., Lefeber, D. J. Gene identification in the congenital disorders of glycosylation type I by whole-exome sequencing. Hum. Molec. Genet. 21: 4151-4161, 2012. [PubMed: 22492991] [Full Text: https://doi.org/10.1093/hmg/dds123]
Wu, X., Rush, J. S., Karaoglu, D., Krasnewich, D., Lubinsky, M. S., Waechter, C. J., Gilmore, R., Freeze, H. H. Deficiency of UDP-GlcNAc:dolichol phosphate N-acetylglucosamine-1 phosphate transferase (DPAGT1) causes a novel congenital disorder of glycosylation type Ij. Hum. Mutat. 22: 144-150, 2003. [PubMed: 12872255] [Full Text: https://doi.org/10.1002/humu.10239]
Wurde, A. E., Reunert, J., Rust, S., Hertzberg, C., Haverkamper, S., Nurnberg, G., Nurnberg, P., Lehle, L., Rossi, R., Marquardt, T. Congenital disorder of glycosylation type Ij (CDG-Ij, DPAGT1-CDG): extending the clinical and molecular spectrum of a rare disease. Molec. Genet. Metab. 105: 634-641, 2012. [PubMed: 22304930] [Full Text: https://doi.org/10.1016/j.ymgme.2012.01.001]