HGNC Approved Gene Symbol: PGM1
SNOMEDCT: 783717008;
Cytogenetic location: 1p31.3 Genomic coordinates (GRCh38): 1:63,593,411-63,660,245 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 1p31.3 | Congenital disorder of glycosylation, type It | 614921 | Autosomal recessive | 3 |
Phosphoglucomutases (PGM; EC 5.4.2.2) catalyze the transfer of phosphate between the 1 and 6 positions of glucose. Isozymes of PGM are monomeric, with molecular masses of about 60 kD, and are encoded by several genes, including PGM1. In most cell types, PGM1 isozymes predominate, representing about 90% of total PGM activity. One exception is red cells, where PGM2 (172000) is a major isozyme (Putt et al., 1993).
Hopkinson and Harris (1966) presented evidence for the existence of at least 2 structural PGM loci, PGM1 and PGM2.
Whitehouse et al. (1992) isolated a cDNA encoding human PGM1. Eighteen amino acid differences were found between human and rabbit PGM1. Southern blot analysis indicated that PGM1 is conserved among a wide variety of vertebrates ranging from primates to birds and amphibia. No evidence for PGM1-related sequences was found either by Southern blot analysis or by in situ hybridization. Thus, if the genes encoding human PGM2 and PGM3 (172100) arose by duplication from the same ancestral gene as PGM1, it seems likely that less than 65% sequence homology has been preserved.
In addition to the ubiquitously expressed Pgm1 transcript, a fast muscle-specific Pgm1 transcript, designated Pgm1fm, exists in rabbit. By PCR using primers derived from the 5-prime end of rabbit Pgm1fm, Putt et al. (1993) isolated human PGM1FM. Human PGM1 and PGM1FM contain alternative first exons, and the deduced PGM1FM protein contains 18 additional N-terminal amino acids compared with PGM1. Human PGM1FM appeared to be expressed at low levels in fast muscle only.
Putt et al. (1993) determined that the PGM1 gene contains 12 exons, including 2 alternative first exons, exons 1A and 1B, that are specific to the ubiquitous PGM1 transcript and the fast muscle PGM1 transcript, respectively. PGM1 spans more than 65 kb, with about 29 kb separating exons 1A and 1B. The region encompassing exon 1A has features characteristic of a housekeeping promoter, including high GC content, high incidence of CpG dinucleotides, lack of TATA or CCAAT boxes, and 6 Sp1 (189906)-binding sites. In contrast, the region encompassing exon 1B is not GC rich, has a low incidence of CpG dinucleotides, and lacks Sp1-binding sites as well as TATA or CCAAT boxes, features consistent with a nonhousekeeping promoter.
Parrington et al. (1968) found that the PGM1, PGM2, and PGM3 genes are not closely linked. By cell hybridization, synteny of PGM1 and peptidase C (PEPC; 170000) was demonstrated by Billardon et al. (1973). These loci are on chromosome 1. Douglas et al. (1973) demonstrated that the PGM1 and 6PGD (PGD; 172200) genes are on the distal end of the short arm of chromosome 1.
Assuming that each arm of chromosome 1 is 140 male cM in length, Cook et al. (1974) concluded that, measured from the centromere, map positions are as follows: PGD 1p124; Rh (see 111680) 1p109; PGM1 1p079; Fy (110700) 1p010, PEPC 1q030. The Goss-Harris method of mapping by radiation-induced gene segregation combines features of recombinational study in families and synteny tests in hybrid cells. As applied to chromosome 1, the method shows that AK2 (103020) and UMPK (CMPK1; 191710) are distal to PGM1 and that the order of the genes is PGM1--UMPK--AK2/alpha-FUC (FUCA1; 612280)--ENO1 (172430) (Goss and Harris, 1977). On the basis of a family segregating for elliptocytosis (611804) and PGD, as well as the common polymorphisms Rh, PGM1, and alpha-fucosidase, Cook et al. (1977) concluded that the map of 1p is, in the male, 1pter--PGD--18%--El--2%--Rh--2%--alpha-FUC--25%--PGM1--centromere. In the female the intervals were estimated to be 22%, 4%, 2%, and 37%, respectively.
The anonymous fragment D1S2 was found to be 7 cM from PGM1 by linkage analysis (Kidd et al., 1988). DNA from somatic cell hybrids containing different portions of chromosome 1 was used for Southern blot analysis, placing D1S2 proximal to 1p32 and distal to PGM1. Kidd et al. (1990) suggested that the somatic cell localization of PGM1 to 1p22.1 may be in error, since linkage studies showed it to be 11.7 cM distal to ACADM (607008), which has been assigned to 1p31 by in situ hybridization.
Whitehouse et al. (1992) assigned the PGM1 gene to chromosome 1p31 by in situ hybridization.
By starch gel electrophoresis, Spencer et al. (1964) demonstrated polymorphism of phosphoglucomutase. Hopkinson and Harris (1966) presented evidence suggesting that PGM1 is responsible for electrophoretically slow-moving components, and at least 5 alleles were identified. PGM2 determines the electrophoretically fast-moving components, and at least 3 alleles may exist at this locus.
By starch gel electrophoresis and by direct determination of activity, Ferrell et al. (1984) detected a deficiency allele at the PGM1 locus. In neither homozygous nor heterozygous state did the null allele have other phenotypic consequences.
Dykes et al. (1985) reported on a nomenclature workshop on PGM1 polymorphisms held in 1983. A total of 30 rare variants were identified and it was recommended that the 4 common alleles be designated as follows: PGM1*1A, PGM1*1B, PGM1*2A, and PGM1*2B.
In the course of paternity testing, Herbich et al. (1985) found an apparent maternal exclusion by the PGM1 enzyme system (mother PGM1 type 1, child PGM1 type 2) and by the Duffy blood group system (mother Fy(a-b+), child Fy(a+b-)). The father was not available for testing. The possibility that the child had been mistakenly identified after birth could be eliminated. The karyotype of the child showed a 'new fragile site' at 1p31, which contains the PGM1 and Duffy loci.
Data on gene frequencies of allelic variants were tabulated by Roychoudhury and Nei (1988).
Takahashi et al. (1982) advanced a phylogeny that attributed 8 alleles of the PGM1 locus to 3 independent mutations in a primal allele, followed by 4 intragenic recombination events involving these mutants. Using the cDNA probes provided by Whitehouse et al. (1992) and Takahashi and Neel (1993), March et al. (1993) confirmed the earlier hypothesis based on protein studies by electrophoresis. The findings were interpreted as strongly supporting the view that only 2 point mutations were involved in the generation of the 4 common alleles and that 1 allele must have arisen by homologous intragenic recombination between these mutation sites.
PGM1 is a highly polymorphic protein. Three mutations and 4 intragenic recombination events between the 3 mutation sites generate 8 protein variants, including the 4 universally common alleles, 1+, 1-, 2+, and 2-, and 4 others that are polymorphic in some Oriental populations, 3+, 3-, 7+, and 7-. The mutations 3/7, 2/1, and +/- are in exons 1A, 4, and 8, and are 40 and 18 kb apart, respectively. Using 12 polymorphic markers, including 2/1 and +/-, Yip et al. (1999) obtained direct evidence for a high rate of intragenic recombination across this 58-kb region. From segregation analysis of PGM1 haplotypes in CEPH families, the recombination frequency was estimated to be 1.7%. Yip et al. (1999) also used a population genetics approach to map the patterns of linkage disequilibrium across the PGM1 gene in 3 diverse population samples (Caucasian, Chinese, and Vietnamese). By this approach they could compare indirect estimates of intragenic recombination with the meiotic data from family studies. Comprehensive pairwise allelic association analysis of the markers indicated the presence of 2 recombination 'hotspots': one between exons 1A and 4 and the other in the region of exon 7. These locations were consistent with the meiotic data and with the original hypothesis of intragenic recombination based on PGM1 isozyme analysis.
Rana et al. (2004) genotyped 264 Caucasian, 222 Chinese, and 187 Vietnamese individuals at 18 SNPs within exons 1A to 4 of the PGM1 gene and constructed haplotypes. Allelic association and haplotype analysis revealed 3 hotspots and 3 haplotype blocks with identical spatial arrangement in all populations studied. The pattern of association within PGM1 represented a region decomposed into small blocks of linkage disequilibrium, where increased recombination activity has disrupted the ancestral chromosome. The authors observed overlap between meiotic crossovers, regions of low linkage disequilibrium, and sequence motifs.
Congenital Disorder of Glycosylation, Type It
In a man with exercise intolerance and episodic rhabdomyolysis resulting from PGM1 deficiency, Stojkovic et al. (2009) identified compound heterozygous mutations in the PGM1 gene (171900.0001 and 171900.0002). Each unaffected parent carried 1 of the mutations. Tegtmeyer et al. (2014) reported follow-up of the patient reported by Stojkovic et al. (2009) and concluded that he had biochemical features consistent with a congenital disorder of glycosylation (CDG1T; 614921).
In 2 unrelated patients with congenital disorder of glycosylation type 1T, Timal et al. (2012) identified 2 different homozygous mutations in the PGM1 gene (171900.0003 and 171900.0004, respectively). The mutations were identified by exome sequencing and confirmed by Sanger sequencing. Transferrin isoelectric focusing in both patients showed abnormal N-glycosylation. In addition to the loss of complete N-glycans, there were minor bands of monosialo- and trisialotransferrin, suggesting the presence of incomplete glycans. Thus, the pattern could best be described as CDGI/II.
In 19 patients from 16 families with CDG1T, Tegtmeyer et al. (2014) identified 21 different homozygous or compound heterozygous mutations in the PGM1 gene (see, e.g., 171900.0005-171900.0009). Three of the patients had previously been reported by Stojkovic et al. (2009) and Timal et al. (2012). The mutation in the first family identified by Tegtmeyer et al. (2014) was found by homozygosity mapping and whole-exome sequencing; mutations in additional families were found by Sanger sequencing. All patients studied had significantly decreased cellular PGM1 enzyme activity (range, 0.3-12% of controls). Patient cells showed considerable variability in the transferrin-glycoform profile, with forms lacking one or both glycans as well as forms with truncated glycans, consistent with a mixed type I/II pattern.
Lee et al. (2014) evaluated 13 missense mutations in the PGM1 gene using a recombinant cellular expression system. Seven missense mutants (N38Y, 171900.0006; L516P, 171900.0005; D62H, 171900.0007; Q41R, G330R, E377K, and E388K) showed significantly reduced expression of soluble protein with increased insoluble protein, indicating increased aggregation. Of the 6 missense mutants that were soluble, 5 (G121R, 171900.0003; D263Y, 171900.0008; T19A, D263G, and G291R) showed significantly impaired catalytic activity (often less than 1% of wildtype), and 1 (T115A; 171900.0001) showed about 50% residual activity. The findings indicated 2 main PGM1-deficient biochemical phenotypes resulting from missense mutations: increased aggregation likely due to folding defects and decreased catalytic activity, with some mutations (e.g., D62H) showing combined defects. All of the mutations affected highly conserved residues.
Conte et al. (2020) reported molecular data on 54 patients with CDG1T, including 11 newly reported and 43 identified in a literature review. Forty-three individual mutations were identified in the PGM1 gene (see, e.g., 171900.0004; 171900.0010-171900.0013). No genotype-phenotype correlation was found.
In a man with congenital disorder of glycosylation type It (CDG1T; 614921), Stojkovic et al. (2009) identified compound heterozygosity for 2 mutations in the PGM1 gene: a 343A-G transition resulting in a thr115-to-ala (T115A) substitution, and a G-to-C transversion in intron 7 resulting in a splice site mutation (IVS7-1G-C; 171900.0002). Each mutation was inherited from an unaffected parent and was not identified in 65 control individuals. The patient had exercise intolerance and episodes of rhabdomyolysis. PGM1 activity represented 1% of control values. Stojkovic et al. (2009) originally reported the patient as having a form of glycogen storage disease (GSD14), but follow-up studies by Tegtmeyer et al. (2014) demonstrated biochemical features consistent with a congenital disorder of glycosylation.
For discussion of the splice site mutation in the PGM1 gene (IVS7-1G-C) that was found in compound heterozygous state in a patient with congenital disorder of glycosylation type It (CDG1T; 614921) by Stojkovic et al. (2009), see 171900.0001.
In a boy of Colombian origin with congenital disorder of glycosylation type It (CDG1T; 614921), Timal et al. (2012) identified a homozygous 415G-C transversion in the PGM1 gene, resulting in a gly121-to-arg (G121R) substitution at a highly conserved residue. Cosegregation of the mutation in the family could not be determined because the child was adopted. The mutation was identified by exome sequencing and confirmed by Sanger sequencing. The patient had dilated cardiomyopathy, cerebral venous thrombosis, and elevated liver enzymes, and died at age 8 years. Studies in patient fibroblasts showed 7% residual enzyme activity.
In a 16-year-old girl with congenital disorder of glycosylation type It (CDG1T; 614921), Timal et al. (2012) identified a homozygous 1507C-T transition in the PGM1 gene, resulting in an arg503-to-ter (R503X) substitution and a truncated protein lacking the last 60 amino acids. Each unaffected parent was heterozygous for the mutation. The mutation was identified by exome sequencing and confirmed by Sanger sequencing. The patient had Pierre Robin sequence with cleft palate, chronic hepatitis, fatigue and dyspnea, and dilated cardiomyopathy. Laboratory studies showed elevated liver enzymes and increased serum creatine kinase. Studies in patient fibroblasts showed 8% residual enzyme activity.
In an Australian patient (patient 2) with CDG1T, Conte et al. (2020) identified compound heterozygous mutations in the PGM1 gene: R503X and an indel mutation (c.157_158delinsG; 171900.0010), predicted to result in a frameshift and premature termination (Gln53GlyfsTer15). The mutations were identified by PGM1 gene sequencing, and the parents were confirmed to be carriers. Functional studies were not performed.
In 2 brothers, born of consanguineous parents, with congenital disorder of glycosylation type It (CDG1T; 614921), Tegtmeyer et al. (2014) identified a homozygous c.1547T-C transition in the PGM1 gene, resulting in a leu516-to-pro (L516P) substitution within the sugar phosphate-binding domain. The mutation, which was found by homozygosity mapping and whole-exome sequencing, segregated with the disorder in the family. The mutation was not found in the dbSNP or Exome Sequencing Project databases. Analysis of cell lines from 1 of the patients showed decreased PGM1 mRNA, and enzymatic activity was 4.4% of controls. The patients had cleft palate and bifid uvula, exercise intolerance, short stature, and abnormal liver enzymes.
In a 9-year-old girl with congenital disorder of glycosylation type It (CDG1T; 614921), Tegtmeyer et al. (2014) identified a homozygous c.112A-T transversion in exon 1A of the PGM1 gene, resulting in an asn38-to-tyr (N38Y) substitution in the PAK1 (602590)-binding region. Patient cells showed decreased PGM1 mRNA and decreased activity (3.1% of controls). The mutation was not found in the dbSNP or Exome Sequencing Project databases. The patient had cleft palate, Pierre-Robin sequence, bifid uvula, increased serum creatine kinase, and abnormal liver enzymes.
In 2 brothers with congenital disorder of glycosylation type It (CDG1T; 614921), Tegtmeyer et al. (2014) identified a homozygous c.184G-C transversion in exon 1A of the PGM1 gene, resulting in an asp62-to-his (D62H) substitution in the PAK1 (602590)-binding region. Patient cells showed 2.1% and 2.8% PGM1 activity levels compared to controls. The mutation was not found in the dbSNP or Exome Variant Server databases. The patients had cleft palate, Pierre-Robin sequence, bifid uvula, short stature, and abnormal liver enzymes.
In a 30-year-old woman with congenital disorder of glycosylation type It (CDG1T; 614921), Tegtmeyer et al. (2014) identified compound heterozygous mutations in the PGM1 gene: a c.787G-T transversion, resulting in an asp263-to-tyr (D263Y) substitution, and a 1-bp deletion (c.661delC; 171900.0009), resulting in a frameshift and premature termination (Arg221ValfsTer13). Patient cells showed 0.3% residual enzymatic activity. Neither mutation was found in the dbSNP or Exome Variant Server databases. The patient had short stature, cleft palate, bifid uvula, abnormal liver enzymes, and exercise intolerance with severely increased serum creatine kinase and rhabdomyolysis.
For discussion of the 1-bp deletion in the PGM1 gene (c.661delC) that was found in a patient with congenital disorder of glycosylation type It (CDG1T; 614921) by Tegtmeyer et al. (2014), see 171900.0008.
For discussion of the c.157_158delinsG mutation in the PGM1 gene, predicted to result in a frameshift and premature termination (Gln53GlyfsTer15), that was found in compound heterozygous state in an Australian patient with congenital disorder of glycosylation type It (CDG1T; 614921) by Conte et al. (2020), see 171900.0004.
In a Pacific Islander (patient 11) with congenital disorder of glycosylation type It (CDG1T; 614921), Conte et al. (2020) identified homozygosity for a c.1561C-T transition in the PGM1 gene, predicted to result in an arg521-to-ter (R521X) substitution and to affect domain IV of the PGM1 gene. The mutation was identified by whole-genome sequencing. The patient had characteristic glycosylation abnormalities identified on mass spectrometry of transferrin.
In an Irish patient (patient 10) with congenital disorder of glycosylation type It (CDG1T; 614921), Conte et al. (2020) identified compound heterozygous mutations in the PGM1 gene: a 2-bp deletion (c.1378_1379delTC) resulting in a frameshift and premature termination (Ala461LysfsTer2), and another 2-bp deletion (c.87_88delCC; 171900.0013) resulting in a frameshift and predicted premature termination (Phe29LeufsTer75). The mutations were identified by sequencing a panel of genes associated with congenital disorders of glycosylation. Functional studies were not performed. (In Table 1 in the article by Conte et al. (2020), this mutation is listed as c.1378_2379delTC.)
For discussion of the c.87_88delCC mutation in the PGM1 gene, predicted to result in a frameshift and premature termination (Phe29LeufsTer75) that was found in compound heterozygous state in an Irish patient with congenital disorder of glycosylation type It (CDG1T; 614921) by Conte et al. (2020), see 171900.0012.
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