HGNC Approved Gene Symbol: POMGNT1
SNOMEDCT: 725043006;
Cytogenetic location: 1p34.1 Genomic coordinates (GRCh38) : 1:46,188,683-46,220,305 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 1p34.1 | Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 3 | 253280 | Autosomal recessive | 3 |
| Muscular dystrophy-dystroglycanopathy (congenital with impaired intellectual development), type B, 3 | 613151 | Autosomal recessive | 3 | |
| Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 3 | 613157 | Autosomal recessive | 3 | |
| Retinitis pigmentosa 76 | 617123 | Autosomal recessive | 3 |
The product of the POMGNT1 gene, protein O-mannose beta-1,2-N-acetylglucosaminyltransferase, participates in O-mannosyl glycan synthesis by transferring N-acetylglucosamine residues to O-linked mannose. O-mannosyl glycan synthesis is essential for the proper functioning of dystroglycan (128239), the central element of the dystrophin-glycoprotein complex (DGC) (summary by Raducu et al., 2012).
By database searches for sequences with similarity to that of GlcNAc-TI (160995), followed by RT-PCR amplification of cDNA fragments from human brain RNA and 5-prime RACE, Yoshida et al. (2001) isolated a human cDNA for protein O-mannose beta-1,2-N-acetylglucosaminyltransferase. The POMGNT1 gene encodes a 660-amino acid type II transmembrane protein, with the region from phe38 to ile58 constituting a putative transmembrane domain. Northern blot analysis detected a 2.7-kb transcript in all 23 normal tissues tested, indicating that human POMGNT1 is constitutively expressed. An additional weaker 3.4-kb band was observed in spinal cord, lymph node, and trachea, suggesting the presence of 2 transcriptional initiation sites or alternative splicing in these tissues.
Zhang et al. (2002) cloned human and mouse POMGNT1, which they termed GNTI.2. The human and mouse proteins share 99% identity over 620 residues. Northern blot analysis revealed wide expression of a 3.3-kb transcript.
Xu et al. (2016) performed immunohistochemistry on adult mouse retina cryosections and observed no expression in the nuclear or plexiform layers. However, there was clear expression in photoreceptor cells, with localization at the basal bodies and daughter centrioles.
Binding and functional analyses by Zhang et al. (2002) indicated that GNTI.2 is specific for alpha-linked terminal Man and does not have MGAT3 (604621), MGAT4B (604561), MGAT5 (601774), MGAT7, or MGAT8 activity.
Raducu et al. (2012) identified functional binding sites in the promoter region of the POMGNT1 gene for the transcription factors SP1 (189906), ETS1 (164720), and GATA (see, e.g., GATA1, 305371).
By genomic PCR analysis of a draft genomic sequence containing human POMGNT1 (GenBank AL360086), Yoshida et al. (2001) determined that the gene is divided into 22 exons and that its coding region begins in exon 2.
Yoshida et al. (2001) noted that the presence of 2 sequence tagged sites in the UniSTS database suggested that the human POMGNT1 gene resides on 1p34-p33.
Muscular Dystrophy-Dystroglycanopathy
Mutation in the POMGNT1 gene can cause 3 different forms of muscular dystrophy-dystroglycanopathy (MDDG): a severe congenital form with brain and eye anomalies (type A3; MDDGA3, 253280), formerly designated Walker-Warburg syndrome (WWS) or muscle-eye-brain disease (MEB); a less severe congenital form with impaired intellectual disability (type B3; MDDGB3; 613151); and a milder limb-girdle form (type C3; MDDGC3; 613157), also known as LGMDR15 and LGMD2O.
Yoshida et al. (2001) identified 6 independent mutations of the POMGNT1 gene (606822.0001-606822.0006) in 6 patients with MEB (see 253280). MEB is an autosomal recessive disorder characterized by congenital muscular dystrophy, ocular abnormalities, and lissencephaly (resulting from a disorder of neuronal migration).
Taniguchi et al. (2003) identified 7 disease-causing mutations in the POMGNT1 gene (see, e.g., 606822.0009; 606822.0011) in 6 non-Finnish Caucasian, Japanese, and Korean patients with suspected MEB. One patient was initially diagnosed clinically as having Fukuyama congenital muscular dystrophy (FCMD; see MDDGA4, 253800), and 2 as having 'atypical' or 'mild' Walker-Warburg syndrome. These 3 diseases are believed to be caused by a similar pathomechanism and thus show clinical overlap. The findings indicated that MEB exists in populations outside of Finland and that the clinical spectrum of MEB is broader than previously recognized. All of the patients with POMGNT1 mutations were still alive contrasting typical WWS, in which almost all patients die before 1 year of age. Mutations were dispersed throughout the entire POMGNT1 gene. A slight correlation was observed between location of the mutation and clinical severity in the brain: patients with mutations near the 5-prime terminus of the POMGNT1 coding region showed relatively severe brain symptoms such as hydrocephalus, while patients with mutations near the 3-prime terminus had milder phenotypes.
Bouchet et al. (2007) identified mutations in the POMT1 gene (607423) in 13 (32%) of 41 families in which at least 1 fetus had severe type II lissencephaly consistent with Walker-Warburg syndrome or MEB. The minimum diagnostic criteria included hydrocephalus, agyria, thickened leptomeninges filled with neuroglial ectopia, disorganized cortical ribbon, and cerebellar dysplasia. Mutations in the POMGNT1 and POMT2 genes (607439) were identified in 6 (15%) and 3 (7%) families, respectively. Overall, mutations were identified in 22 of 41 families included in the study. Patients with POMGNT1 mutations had a relatively less severe phenotype. Definitive pathogenic mutations were not identified in the FKRP (606596), FKTN (607440), or LARGE (603590) genes.
Hehr et al. (2007) identified 9 POMGNT1 mutations, including 6 novel mutations, in 9 MEB patients from 8 unrelated families of various ethnic origins. The authors noted that 34 different POMGNT1 mutations had been identified in MEB patients; most are predicted to result in complete loss of enzyme activity. The data suggest mutation hotspots within the minimal catalytic domain at arg442 in exon 16, and in intron 17. No genotype-phenotype correlations were observed.
In an Irish girl with limb-girdle muscular dystrophy and normal intellect (MDDGC3; 613157), Clement et al. (2008) identified a homozygous mutation in the POMGNT1 gene (D556N; 606822.0013).
Godfrey et al. (2007) identified POMGNT1 mutations in 7 of 92 patients with evidence of a muscular dystrophy due to defective glycosylation of alpha-dystroglycan (DAG1; 128239). One patient had WWS, 5 had MEB, and 1 had limb-girdle congenital muscular dystrophy without mental retardation (same patient as reported by Clement et al., 2008).
Mercuri et al. (2009) identified POMGNT1 mutations in 8 (10%) of 81 Italian patients with a dystroglycanopathy. One patient had Walker-Warburg syndrome, 6 had muscle-eye-brain disease, and 1 had congenital muscular dystrophy with mental retardation and cerebellar cysts (MDDGB3; 613151). The last patient had a homozygous missense mutation (R605P; 606822.0014). All had mental retardation and structural brain abnormalities; most had eye involvement. In general, the more severe phenotypes appeared to be associated with mutations predicted to result in severe disruption of the gene.
Retinitis Pigmentosa 76
In 4 affected individuals from 3 unrelated families with nonsyndromic retinitis pigmentosa (RP76; 617123), Xu et al. (2016) identified biallelic mutations in the POMGNT1 gene (606822.0018-606822.0022). Reexamination of all 4 patients revealed no extraocular features.
In 5 families with nonsyndromic RP from a closed community on a small Taiwanese island, Wang et al. (2016) identified a homozygous missense mutation in the POMGNT1 gene (L120R; 606822.0023) that segregated fully with disease and was not found in controls.
Diesen et al. (2004) identified a splice site mutation in intron 17 (606822.0002) as a founder mutation in the Finnish population; it was present in 18 of 19 Finnish MEB patients. Phenotypic variability was observed among the 18 homozygous Finnish patients, suggesting that other factors contribute to the pathogenesis of the disorder.
In eukaryotes, proteins are frequently modified by O-glycosylation as well as by N-glycosylation. O-glycosylation occurs at serine and threonine residues. In yeast and fungi, O-glycosylation occurs mainly in the form of O-mannosylation. However, O-mannosylation is rare in mammals, occurring in a limited number of glycoproteins of brain, nerve, and skeletal muscle (Endo, 1999). Grewal et al. (2001) found that a deletion of a glycosyltransferase-like protein gene, Large (603590), is the basis of the myodystrophy (myd) mouse and gives rise to an alpha-dystroglycan (128239) that is markedly underglycosylated. Hayashi et al. (2001) found that muscle from patients with Fukuyama-type congenital muscular dystrophy, which has as its primary defect mutations in fukutin (a protein encoded by a gene on 9q31), shows a selective deficiency of highly glycosylated alpha-dystroglycan. These findings suggested that interference in glycosylation is one cause of muscular dystrophies. The finding that mutations in POMGNT1 result in MEB provided a molecular basis for the defects in O-mannosyl glycan synthesis and suggested that interference in O-mannosyl glycosylation is a pathomechanism for muscular dystrophy as well as neuronal migration disorder (Yoshida et al., 2001).
Kano et al. (2002) reported a selective deficiency of alpha-dystroglycan in MEB patients. This finding suggested that alpha-dystroglycan is a target of POMGNT1 and that altered glycosylation of DAG1 may play a critical role in the pathomechanism of MEB.
In 2 unrelated patients with muscle-eye-brain disease (MDDGA3; 253280), each the offspring of consanguineous parents, Yoshida et al. (2001) identified a splice site mutation (IVS17DS+1G-T) in the POMGNT1 gene, leading to deletion of amino acids leu472 to his513. Each patient was homozygous for the mutation.
In a patient with muscle-eye-brain disease (MDDGA3; 253280), born of consanguineous parents, Yoshida et al. (2001) found a homozygous IVS17+1G-A splice donor site mutation in the POMGNT1 gene. The mutation generated 2 different mRNAs: a read-through of intron 17 with introduction of a termination codon at 484 and a skipping of exon 17 resulting in an in-frame deletion of 42 amino acids. Both transcripts resulted in less than 1% residual enzyme activity.
Taniguchi et al. (2003) determined that a Japanese American girl with hypotonia, high VEP, cataracts, cerebellar vermis hypoplasia, and type II lissencephaly was a compound heterozygote for 2 mutations in the POMGNT1 gene: IVS17DS+1G-A and a 1-bp deletion (606822.0011). Her father, who carried the IVS17 mutation, was of Scandinavian origin. She had initially been diagnosed with 'mild' Walker-Warburg syndrome, but the molecular analysis confirmed MEB.
Diesen et al. (2004) referred to this mutation as 1539+1G-A and identified it as a founder mutation in the Finnish population; it was present in 18 of 19 Finnish MEB patients. Phenotypic variability was observed among the 18 homozygous Finnish patients, suggesting that other factors contribute to the pathogenesis.
In several affected sibs with muscle-eye-brain disease (MDDGA3; 253280), Yoshida et al. (2001) found a homozygous 1743G-A transition in exon 19 of the POMGNT1 gene, resulting in a ser550-to-asn (S550N) substitution.
In a patient with muscle-eye-brain disease (MDDGA3; 253280) who was the son of consanguineous parents, Yoshida et al. (2001) found homozygosity for a 1-bp deletion at base 1813 in exon 20, causing a frameshift and a premature termination at residue 633.
In a patient with muscle-eye-brain disease (MDDGA3; 253280) who was the son of nonconsanguineous parents, Yoshida et al. (2001) found compound heterozygosity for mutations in the POMGNT1 gene: a pro493-to-arg (P493R) missense mutation resulting from a 1572C-G transversion in exon 17, and a 1-bp deletion (1970delG) in exon 21 that caused a frameshift and premature stop at residue 633 (606822.0006).
See 606822.0005 and Yoshida et al. (2001).
In 2 affected sibs from a non-Finnish family with muscle-eye-brain disease (MDDGA3; 253280), Vervoort et al. (2004) identified compound heterozygosity for 2 mutations in the POMGNT1 gene: a 1465C-T transition in exon 16, resulting in an arg442-to-cys (R442C) substitution, and a 1073G-A transition in exon 10, resulting in an arg311-to-gln substitution (R311Q; 606822.0008). The R442C and R311Q mutations are in the highly conserved GNT1 domain of the protein. Each parent was heterozygous for 1 of the mutations.
See 606822.0007 and Vervoort et al. (2004).
In an Italian patient with muscle and brain abnormalities consistent with MEB disease (MDDGA3; 253280) but without eye abnormalities, Biancheri et al. (2006) identified homozygosity for a 932G-A transition in exon 10 of the POMGNT1 gene, resulting in an arg311-to-gln (R311Q) substitution. She had an unusual phenotype with relatively late onset (age 22 months, not at birth), mildly increased serum creatine kinase, and absence of ocular abnormalities. At age 30 years, she was mentally retarded and had seizures, but was able to walk without muscle weakness. Brain MRI showed cortical dysplasia and brainstem hypoplasia.
Taniguchi et al. (2003) determined that an Italian girl with congenital muscular dystrophy, retinal dysplasia, cerebellar vermis hypoplasia, type II lissencephaly, and hydrocephalus consistent with MEB (MDDGA3; 253280) was homozygous for a 281C-T transition in POMGNT1, resulting in an arg63-to-ter (R63X) substitution. She had initially been diagnosed with 'atypical' Walker-Warburg syndrome.
In an Italian patient with a diagnosis of Walker-Warburg syndrome (MDDGA3; 253280), Mercuri et al. (2009) identified a homozygous R63X mutation. Although clinical details were limited, the patient had severely impaired motor development, microcephaly, and mental retardation, but could sit with support. The patient also had 25-fold increased serum creatine kinase, seizures, myopia, and retinal dysplasia. Brain MRI findings were consistent with WWS, as defined by severe lissencephaly, hydrocephalus, and cerebellar and corpus callosum involvement.
In a Japanese American girl with hypotonia, high VEP, cataracts, cerebellar vermis hypoplasia, and type II lissencephaly consistent with MEB (MDDGA3; 253280), Taniguchi et al. (2003) identified compound heterozygosity for 2 mutations in the POMGNT1 gene: a 1-bp deletion (1926delT) in exon 21 and a splice site mutation (606822.0002).
In a patient with Walker-Warburg syndrome (MDDGA3; 253280), Godfrey et al. (2007) identified a homozygous 1425G-A transition in exon 17 of the POMGNT1 gene, resulting in a trp475-to-ter (W475X) substitution. Although clinical details were limited, the patients had neonatal onset, and never achieved sitting. They also had low IQ and increased serum creatine kinase. Brain MRI showed cerebellar hypoplasia, cerebellar cysts, white matter abnormalities, hydrocephalus, and lissencephaly.
In an Irish girl with limb-girdle muscular dystrophy and normal intellect (MDDGC3; 613157), Clement et al. (2008) identified a homozygous 1666G-A transition in exon 20 of the POMGNT1 gene, resulting in an asp556-to-asn (D556N) substitution. In vitro functional expression studies showed normal POMGNT1 activity in conventional assays, but altered kinetic properties.
In a patient with congenital muscular dystrophy, mental retardation, and cerebellar cysts on brain MRI (MDDGB3; 613151), Mercuri et al. (2009) identified a homozygous 1814G-C transversion in exon 21 of the POMGNT1 gene, resulting in an arg605-to-pro (R605P) substitution. The patient was identified in a larger study of 81 patients with muscular dystrophy and evidence of a dystroglycanopathy. Although clinical details were limited, the patient had achieved walking, showed decreased alpha-dystroglycan on muscle biopsy, and had strabismus, myopia, and mental retardation. Brain MRI showed cerebellar cysts.
In a 16-year-old patient with POMGNT1-related congenital muscular dystrophy (MDDGB3; 613151), Clement et al. (2008) identified compound heterozygosity for 2 mutations in the POMGNT1 gene: a 652+1G-A transition, presumably resulting in a splice site mutation, and a cys490-to-tyr (C490Y; 606822.0016) substitution. The patient had mental retardation, myopia, optic atrophy, and increased serum creatine kinase. Brain MRI showed ventricular dilatation, diffuse white matter changes, cerebellar cysts, and pontine hypoplasia. Genetic analysis identified compound heterozygosity for 2 mutations in the POMGNT1 gene (606822.0015 and 606822.0016).
See 606822.0015 and Clement et al. (2008).
In an 11-year-old Belgian boy with limb-girdle muscular dystrophy without brain or eye anomalies (MDDGC3; 613157), Raducu et al. (2012) identified a homozygous 9-bp duplication (-83_-75dup) upstream of the transcriptional start site of the POMGNT1 gene in the 5-prime flanking region. Each unaffected parent was heterozygous for the mutation, which was not found in 200 control individuals. Transfection of the mutation in COS-7 and HEK293T cells resulted in a 75% decrease in promoter activity compared to wildtype. Electrophoretic mobility shift assay (EMSA) revealed binding sites for several transcription factors in this region. The mutation generated an additional binding site for the transcriptional repressor ZNF202 (603430), resulting in the downregulation of POMGNT1 gene expression and, ultimately, defective glycosylation. The patient had slightly delayed initial motor development and had unsteady standing at age 2 years. He had muscle weakness, slight generalized amyotrophy, a positive Gowers sign, and lack of reflexes. At age 7 to 8 years, he had lumbar hyperlordosis, difficulties in climbing stairs, and weakness of the shoulder muscles. Laboratory studies showed a mild elevation of serum creatine kinase, and muscle biopsy showed dystrophic changes and defects in alpha-dystroglycan staining.
In a 78-year-old Italian woman and her 69-year-old brother with nonsyndromic retinitis pigmentosa (RP76; 617123), Xu et al. (2016) identified compound heterozygosity for mutations in the POMGNT1 gene: a c.860T-G transversion (c.860T-G, NM_017739), resulting in an ile287-to-ser (I287S) substitution at a highly conserved residue, and a c.187C-T transition, resulting in an arg63-to-ter (R63X; 606822.0019) substitution. An unaffected sister was heterozygous for the missense mutation, and an unaffected brother did not carry either mutation. The nonsense mutation was not found in the ExAC database, whereas the missense mutation was present at a frequency of 1 in 40,000. Functional analysis in transfected HEK293T cells demonstrated that the I287S mutation retained only 10% of the activity of wildtype, indicating that I287S represents a hypomorphic mutation.
For discussion of the c.187C-T transition (c.187C-T, NM_017739) in the POMGNT1 gene, resulting in an arg63-to-ter (R63X) substitution, that was found in compound heterozygous state in an Italian sister and brother with nonsyndromic retinitis pigmentosa (RP76; 617123) by Xu et al. (2016), see 606822.0018.
In a 32-year-old woman from a consanguineous Han Chinese family with nonsyndromic retinitis pigmentosa (RP76; 617123), Xu et al. (2016) identified homozygosity for a c.466G-A transition (c.466G-A, NM_017739) in the POMGNT1 gene, resulting in a glu156-to-lys (E156K) substitution at a highly conserved residue. Segregation analysis was not reported. The mutation was not found in the ExAC database, and the authors noted that it had not been detected in patients with muscular dystrophy-dystroglycanopathy. Functional analysis in transfected HEK293T cells demonstrated that the E156K mutation retained only 30% of the activity of wildtype, indicating that E156K represents a hypomorphic mutation.
In a 52-year-old Han Chinese man with nonsyndromic retinitis pigmentosa (RP76; 617123), Xu et al. (2016) identified compound heterozygosity for mutations in the POMGNT1 gene: a c.1895+1G-A transition (c.1895+1G-A, NM_017739) in intron 21, resulting in premature termination (V633X), and a c.1505G-C transversion, resulting in a gly502-to-ala (G502A) substitution at a highly conserved residue. Neither mutation was found in the ExAC database. Xu et al. (2016) stated that the splice site mutation had previously been identified (Diesen et al., 2004; Saredi et al., 2012) in compound heterozygosity in 2 unrelated patients with muscular dystrophy-dystroglycanopathy (253280), and was reported to cause intron retention and generation of a premature stop codon.
For discussion of the c.1505G-C transversion (c.1505G-C, NM_017739) in the POMGNT1 gene, resulting in a gly502-to-ala (G502A) substitution, that was found in compound heterozygous state in a patient with nonsyndromic retinitis pigmentosa (RP76; 617123) by Xu et al. (2016), see 606822.0021.
In 17 affected individuals from 5 families with nonsyndromic retinitis pigmentosa (RP76; 617123) from a closed community on a small Taiwanese island, Wang et al. (2016) identified homozygosity for a c.359A-C transversion (c.359A-C, NM_017739.3) in exon 5 of the POMGNT1 gene, resulting in a leu120-to-arg (L120R) substitution at a highly conserved residue. The mutation segregated fully with disease in the families, and was not found in 470 Han Chinese controls. Functional analysis in HEK293T cells demonstrated that the L120R mutant had only 21% of the enzymatic activity of wildtype.
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