Common glucose-6-phosphate dehydrogenase (G6PD) variants from the Italian population: biochemical and molecular characterization

Functional interpretation, cataloging, and analysis of 1,341 glucose-6-phosphate dehydrogenase variants

Glucose-6-phosphate dehydrogenase (G6PD) deficiency affects over 500 million individuals who can experience anemia in response to oxidative stressors such as certain foods and drugs. Recently, the World Health Organization (WHO) called for revisiting G6PD variant classification as a priority to implement genetic medicine in low- and middle-income countries. Toward this goal, we sought to collect reports of G6PD variants and provide interpretations. We identified 1,341 G6PD variants in population and clinical databases. Using the ACMG standards and guidelines for the interpretation of sequence variants, we provided interpretations for 268 variants, including 186 variants that were not reported or of uncertain significance in ClinVar, bringing the total number of variants with non-conflicting interpretations to 400. For 414 variants with functional or clinical data, we analyzed associations between activity, stability, and current classification systems, including the new 2022 WHO classification. We corroborated known challenges with classification systems, including phenotypic variation, emphasizing the importance of comparing variant effects across individuals and studies. Biobank data made available by All of Us illustrate the benefit of large-scale sequencing and phenotyping by adding additional support connecting variants to G6PD-deficient anemia. By leveraging available data and interpretation guidelines, we created a repository for information on G6PD variants and nearly doubled the number of variants with clinical interpretations. These tools enable better interpretation of G6PD variants for the implementation of genetic medicine.

Glucose-6-phosphate dehydrogenase (G6PD) mutations database: review of the "old" and update of the new mutations

In the present paper we have updated the G6PD mutations database, including all the last discovered G6PD genetic variants. We underline that the last database has been published by Vulliamy et al. [1] who analytically reported 140 G6PD mutations: along with Vulliamy's database, there are two main sites, such as http://202.120.189.88/mutdb/ and www.LOVD.nl/MR, where almost all G6PD mutations can be found. Compared to the previous mutation reports, in our paper we have included for each mutation some additional information, such as: the secondary structure and the enzyme 3D position involving by mutation, the creation or abolition of a restriction site (with the enzyme involved) and the conservation score associated with each amino acid position. The mutations reported in the present tab have been divided according to the gene's region involved (coding and non-coding) and mutations affecting the coding region in: single, multiple (at least with two bases involved) and deletion. We underline that for the listed mutations, reported in italic, literature doesn't provide all the biochemical or bio-molecular information or the research data. Finally, for the "old" mutations, we tried to verify features previously reported and, when subsequently modified, we updated the specific information using the latest literature data.

Multi-mutational analysis of fifteen common mutations of the glucose 6-phosphate dehydrogenase gene in the Mediterrranean population

BACKGROUND

Glucose-6-phosphate dehydrogenase (G6PD) is a cytosolic enzyme encoded by a housekeeping X-linked gene whose main function is to produce NADPH, a key electron donor in the defence against oxidizing agents and in reductive biosynthetic reactions. Many variants of G6PD have been described, mostly produced from missense mutations, with wide ranging levels of enzyme activity and associated clinical symptoms.

METHOD

A single base extension assay is used, yielding a single base difference of the extended products. Primers are designed to amplify products of different sizes with distinct fluorescent dyes in order to accurately distinguish all possible combinations of genotypes (homozygous and heterozygous for each mutation) in a multiplex PCR analysis.

RESULTS

We present the first application of a multiplex multicolour assay to detect 15 of the most frequent G6PD-related mutations in Spain, which are studied in three multiplex reactions. Capillary electrophoresis analysis of the amplified products enables easy, rapid, unambiguous and high-resolution discrimination between wild-type and mutant alleles, even though various mutations may be present in the multiplex analysis.

CONCLUSION

The analytical method described herein offers greater diagnostic power in Spanish and Mediterranean populations and would facilitate automated genotyping in routine molecular diagnostics and large-scale genetic studies (e.g., newborn screening programs).

A comprehensive study on the major mutations in glucose-6-phosphate dehydrogenase-deficient polymorphic variants identified in the coastal provinces of Caspian Sea in the north of Iran

BACKGROUND

The aim of this study was the molecular analysis of G6PD patients for G6PD mutations in the coastal provinces of the Caspian Sea in north of Iran.

METHODS

Studies on G6PD deficiency in the coastal provinces of the Caspian Sea in Iran were performed in 248 patients with a history of favism, in Mazandaran, Golestan and Gillan provinces, which contributed 74, 71 and 103 samples, respectively. Three different major polymorphic variants were determined by molecular analysis, using SSCP, sequencing and PCR-RFLP methods. Firstly, all Mazandaranian samples were searched for the Mediterranean mutation by PCR-RFLP method. The remaining samples of the Mazandaran province were analysed by SSCP followed by sequencing for other mutations. Then, our research was expanded in two other provinces, Golestan and Gillan, by the PCR-RFLP method.

RESULTS

Three different major polymorphic variants were found: G6PD Mediterranean 75.4% (187 out of 248), G6PD Chatham 19.76% (49 out of 248), G6PD Cosenza 2.02% (5 out of 248) and 7 samples out of 248 remained unknown. Also, there was no significant difference in the incidence of various G6PD polymorphic variants with mean age, and various blood work values such as Hb, WBC and MCV between two major variants (p>0.20).

CONCLUSIONS

These results which are the first molecular investigation in north of Iran indicate a higher prevalence of G6PD Chatham in this large Iranian population than anywhere else in the world. The distribution of these G6PD variants is more similar to that found in an Italian population (80-84% for Mediterranean, 20% for Chatham and 1.9% for Cosenza mutation). Although the origin of Iranian population is rather uncertain, the closer similarity of the mutation spectrum to Italian rather than Middle Eastern population may indicate that these populations have a common ancestral origin.

Molecular identification of mutations in G6PD gene in patients with favism in Iran

Glucose 6-phosphate dehydrogenase is a highly polymorphic enzyme encoded by a human X-linked gene (Xq2.8). This enzyme catalyses the first step of pentose phosphate pathway, that converts glucose 6-phosphate to 6-phosphogluconate with production of NADPH2. G6PD deficiency is the most common human metabolic inborn error affecting more than 400 million people world wide. The main clinical manifestations are acute hemolytic anemia and jaundice, triggered by infection or ingestion of Fava beans or oxidative drugs. A predominant variant of G6PD named Mediterranean is often associated with favism. This has been evident in several countries including Northern coastal provinces of Iran. Other current variants are Chatham and Cosenza. Molecular identification of the most prevalent mutations in G6PD gene was carried out in 71 males and females with G6PD deficiency. They were from Iranian Northern province of Golestan. DNA was extracted from blood samples and analyzed for known G6PD mutation by PCR and restriction fragment length polymorphisms (RFLP) technique. Adapting this method, revealed that Mediterranean mutation at nt 563(C-->T) is predominant in the area (69%) and 26.7% of patients have Chatham mutation at nt 1003(G-->A). Findings indicate a higher prevalence of these mutations, in Golestan compared to Mazandaran (66.2% Mediterranean and 19% Chatham mutation) and Gilan (86.4% Mediterranean and 9.71% Chatham mutations). Cosenza mutation at nt 1376(G-->C), by PCR-RFLP technique was not found among other 3 samples (4.3%). The similarity of these results with mutations in Italy indicates probable existence of a common ancestral origin in the observed populations.

Bilirubin levels in the acute hemolytic crisis of G6PD deficiency are related to Gilbert's syndrome

In this study we analyzed the effect of the (TA)7 polymorphism of the UGT1A gene associated with Gilbert's syndrome in G6PD-deficient subjects during an acute hemolytic crisis (fabic crisis). DNA from 44 subjects originating from the same geographic area in Sardinia was analyzed for the UGT1A promoter polymorphism. The increase of unconjugated bilirubin level during fabic crisis and its relationship with UGT1A polymorphism was evaluated. The UGT1A (TA)7 TATA box variant was found in 9/44 (21%) of the G6PD deficient subjects examined. The median value for unit of increase of bilirubin (mg/dl)/unit of decrease of hemoglobin (g/dl) was higher in variant homozygous than in heterozygous and normal subjects. These findings imply a contribution of the UGT1A polymorphism associated to Gilbert's syndrome to development of the hyperbilirubinemia in G6PD deficient subjects during acute hemolytic anemia.

Red blood cell enzymes and their clinical application

Red blood cell enzyme activities are measured mainly to diagnose hereditary nonspherocytic hemolytic anemia associated with enzyme anomalies. At least 15 enzyme anomalies associated with hereditary hemolytic anemia have been reported. Some nonhematologic disease can also be diagnosed by the measurement of red blood cell enzyme activities in the case in which enzymes of red blood cells and the other organs are under the same genetic control. Progress in molecular biology has provided a new perspective. Techniques such as the polymerase chain reaction and single-strand conformation polymorphism analysis have greatly facilitated the molecular analysis of erythroenzymopathies. These studies have clarified the correlation between the functional and structural abnormalities of the variant enzymes. In general, the mutations that induce an alteration of substrate binding site and/or enzyme instability might result in markedly altered enzyme properties and severe clinical symptoms.

Molecular Analysis of Eight Biochemically Unique Glucose-6-Phosphate Dehydrogenase Variants Found in Japan

We analyzed the molecular mutations of eight known Japanese glucose-6-phosphate dehydrogenase (G6PD) variants with unique biochemical properties. Three of them were caused by novel missense mutations: G6PD Musashino by 185 C→T, G6PD Asahikawa by 695 G→A, and G6PD Kamiube by 1387 C→T. Predicted amino acid substitutions causing asymptomatic variants G6PD Musashino (62 Pro→Phe) and G6PD Kamiube (463 Arg→Cys) were located in regions near the amino or carboxyl end of the polypeptide chain, whereas an amino acid change 232 Cys→Tyr causing a class 1 variant G6PD Asahikawa was located in the region where amino acid alterations in some class 1 variants were clustered. The other five variants had known missense mutations, namely, G6PD Fukushima, 1246 G→A, G6PD Morioka, 1339 G→A, and G6PD Iwate, G6PD Niigata and G6PD Yamaguchi, 1160 G→A, which cause variants, G6PD Tokyo, G6PD Santiago de Cuba, and G6PD Beverly Hills, respectively.

Molecular basis of erythroenzymopathies associated with hereditary hemolytic anemia: tabulation of mutant enzymes

Molecular abnormalities of erythroenzymopathies associated with hereditary hemolytic anemia have been determined by means of molecular biology. Pyruvate kinase (PK) deficiency is the most common and well-characterized enzyme deficiency in the glycolytic pathway, and it causes hereditary hemolytic anemia. To date, 47 gene mutations have been identified. We identified one base deletion, one splicing mutation, and six distinct missense mutations in 12 unrelated families with a homozygous PK deficiency. Mutations located near the substrate or fructose-1,6- diphosphate binding site may change the conformation of the active site, resulting in a drastic loss of activity and severe clinical symptoms. Glucose-6-phosphate dehydrogenase (G6PD)deficiency is the most common metabolic disorder, and it is associated with chronic hemolytic anemia and/or drug- or infection-induced acute hemolytic attack. An estimated 400 million people are affected worldwide. The mutations responsible for about 78 variants have been determined. Some have polymorphic frequencies in different populations. Most variants are produced by one or two nucleotide substitutions. Molecular studies have disclosed that most of the class 1 G6PD variants associated with chronic hemolysis have the mutations surrounding either the substrate or the NADP binding site. Among rare enzymopathies, missense mutations have been determined in deficiencies of glucosephosphate isomerase, (TPI), phosphoglycerate kinase, and adenylate kinase. Compound heterozygosity with missense mutation and base deletion has been determined in deficiencies of hexokinase and diphosphoglyceromutase. Compound heterozygosity with missense and nonsense mutations has been identified in TPI deficiency. One base junction mutations resulting in abnormally spliced PFK-M mRNA have been identified in homozygous PFK deficiency. An exception is hemolytic anemia due to increased adenosine deaminase activity. The basic abnormality appears to result from the overproduction of a structurally normal enzyme.

Muscle expression of glucose-6-phosphate dehydrogenase deficiency in different variants

Muscle expression of G6PD deficiency has been investigated in Mediterranean, Seattle-like and A-variants. G6PD activity was detected in samples obtained from biopsies on the quadriceps muscle of seven males and one female. The type of genetic variant was determined by molecular analysis of DNA, extracted from blood samples. All variants showed the enzyme defect in muscle. A statistically significant relationship was found in the activity of G6PD between erythrocytes and muscle of the male subjects (r = 0.968; p = 0.00008). The equation for the best fit line was: Y = 0.390X + 0.198. The results suggest that, for a given variant, the extent of the enzyme defect in muscle may be determined, using this equation, from the G6PD activity of erythrocytes.

A novel single-base mutation in the glucose 6-phosphate dehydrogenase gene is associated with chronic non-spherocytic haemolytic anaemia

More than 80 variants of glucose-6-phosphate dehydrogenase (G6PD) are associated with chronic nonspherocytic haemolytic anaemia (CNSHA); however, the molecular basis of this association is not fully understood. We have used the polymerase chain reaction and nucleotide sequence analysis to characterize a new G6PD variant, which we designate as G6PD Bari, in a G6PD-deficient boy affected by CNSHA. A single mutation leading to an amino-acid substitution was detected in the G6PD coding region, viz. a C->T transition at position 1187 predicting leucine at residue 396 in the enzyme; proline is invariably present in evolutionary distant G6PD molecules at this position. Inheritance in the patient's family was demonstrated by the polymerase chain reaction followed by diagnostic restriction enzyme analysis. The C->T transition responsible for G6PD Bari maps close to several other mutations previously identified in G6PD variants associated with CNSHA.

Variants of glucose-6-phosphate dehydrogenase are due to missense mutations spread throughout the coding region of the gene

Glucose-6-phosphate dehydrogenase (G6PD) is remarkable for its genetic diversity in humans. Many variants of G6PD have been described with wide ranging levels of enzyme activity and associated clinical symptoms. Fifty-eight different mutations have now been identified and these account for 97 named G6PD variants. The mutations are almost exclusively missense mutations, causing single amino acid substitutions. They are spread throughout the coding region of the gene, although there appears to be a cluster of mutations that cause a more severe clinical phenotype towards the 3' end of the gene. The absence of large deletions, frameshift mutations and nonsense mutations is consistent with the notion that a total lack of G6PD activity would be lethal.

Study of glucose-6-phosphate dehydrogenase: history and molecular biology

Glucose-6-phosphate dehydrogenase (G6PD) deficiency was discovered in the 1950s. The history of the development of knowledge about G6PD deficiency is reviewed here. In the first decade after its discovery, the clinical manifestations of G6PD deficiency began to be understood. In the second decade, attention was focused on the degree of variability of this enzyme and the distinction of the various biochemical variants from one another. In the last decade, it has been possible to understand the mutations that effect this enzyme at the DNA level. Some 40 different mutations have now been characterized. Analysis of these mutations indicates that, while diversity sometimes exists within a mutation considered biochemical homogeneous, more often variants thought to be distinct prove to be identical. The study of G6PD mutations is beginning to provide insight into structure-function relationships.

Alpha I/65 hereditary elliptocytosis in southern Italy: evidence for an African origin

alpha I/65 Hereditary elliptocytosis (HE) is due to the duplication of TTG codon 154 (leucine) of alpha-spectrin and is associated with a constant haplotype. It was encountered exclusively in African and American Blacks, and in North Africans. We assumed that it diffused from the Benin-Togo area to Northern Africa. We now report two South Italian families with alpha I/65 HE. The phenotype fully conformed to previous descriptions. The mode of transmission was dominant; however, the manifestations were more pronounced when the common, low expression level alpha V/41 allele occurred in trans to the alpha I/65 allele, also conforming to previous records. The mutation underlying alpha I/65 HE turned out to be, again, the duplication of TTG codon 154 and the associated haplotype was the same as that encountered previously (+-+; XbaI, PvuII, MspI). Thus, the alpha I/65 allele found in Italy must have been introduced from North Africa across the Sicilian channel and would ultimately have originated from the Benin-Togo area. It would witness the same migratory stream as that followed by the Benin type haemoglobin S allele, which is also present in Southern Italy.

Molecular heterogeneity underlying the G6PD Mediterranean phenotype

As part of a study aiming to define the molecular basis of glucose-6-phosphate dehydrogenase (G6PD) deficiency, we analysed a sample from a Portugese boy with a family history of favism. Although the biochemical properties of red-cell G6PD from this subject were similar to those of the common variant G6PD Mediterranean, the corresponding mutation (563 C----T) was not present. Instead, polymerase chain reaction (PCR) amplification and sequencing of the entire gene detected a C----T transition at nucleotide 592 in exon VI, changing an arginine residue to a cysteine residue only 10 amino acids downstream from the Mediterranean mutation. Single-strand conformation polymorphism analysis of a PCR-amplified DNA fragment spanning exons VI and VII of the G6PD gene has detected the same mutation, confirmed by sequencing, in a G6PD-deficient patient from Southern Italy. We name this new variant G6PD Coimbra.

Molecular basis of chronic non-spherocytic haemolytic anaemia: a new G6PD variant (393 Arg----His) with abnormal KmG6P and marked in vivo instability

More than 80 genetic variants of glucose-6-phosphate dehydrogenase (G6PD) are associated with chronic non-spherocytic haemolytic anaemia (CNSHA). In order to help clarify the molecular basis of this association, we have carried out a detailed biochemical and genetic characterization of two G6PD deficient brothers affected by CNSHA. The G6PD from the two patients has altered electrophoretic mobility, abnormally elevated Michaelis constant (Km) for G6P, and extreme instability in vivo and in vitro. By comparison with published information we found that this is a new G6PD variant which we have designated G6PD Portici. The entire coding region of the gene has been sequenced, and a single point mutation, a G----A transition, was found at position 1178 in exon X, causing a substitution of histidine for arginine at residue 393 in the polypeptide chain. By polymerase chain reaction (PCR) amplification followed by diagnostic restriction enzyme analysis and allele-specific oligonucleotide hybridization we have demonstrated the inheritance of this mutation in the patient's family. Our results support the notion of a causative link between this mutation in the G6PD gene and CNSHA. Our data, in combination with previous data in the literature, suggest that the three-dimensional structure of G6PD is such as to cause interaction in the binding of its two substrates, G6P and NADP.

Two commonly occurring nucleotide base substitutions in Chinese G6PD variants

Using a direct PCR sequencing technique, we have identified two DNA base substitutions in 8 different biochemical G6PD variants of Chinese origin. Neither one of these abnormalities has been reported in other ethnic groups. An abnormality (C1) of G to T substitution at cDNA 1376 causing an amino acid change from Arg to Leu has been found in 3 variants. Another abnormality (C2) of G to A substitution at cDNA 1388 causing an amino acid change from Arg to His has been found in 5 variants. Both C1 and C2 are located in exon 12 of the G6PD gene and are only 12 base pairs apart. However, C1 is associated with a significant increase in the deamino-NADP utilization rate, whereas C2 is not. Taken together, our data suggest that C1 and C2 are very common among Chinese with a G6PD deficiency and exon 12 may define an important functional domain of the human G6PD.

Sequence of human glucose-6-phosphate dehydrogenase cloned in plasmids and a yeast artificial chromosome

The sequence of 20,114 bp of DNA including the human glucose-6-phosphate dehydrogenase (G6PD) gene was determined. The region included a prominent CpG island, starting about 680 nucleotides upstream of the transcription start site, extending about 1050 nucleotides downstream of the start site, and ending just at the start of the first intron. The transcribed region from the start site to the poly(A) addition site covers 15,860 bp. The sequence of the 13 exons agreed with published cDNA sequence and for the 11 exons tested, with the corresponding sequence in a yeast artificial chromosome (YAC). The latter confirms YAC cloning fidelity at the DNA sequence level. Sixteen Alu sequences constitute 24% of the total sequence tract. Four were outside the borders of the mRNA transcript of the gene; all the others were found in a large (9858 bp) intron between exons 2 and 3. Two Alu clusters each contain Alus lying between the monomers of another.

Identification of a single base change in a new human mutant glucose-6-phosphate dehydrogenase gene by polymerase-chain-reaction amplification of the entire coding region from genomic DNA

We report the characterization at the molecular level of a mutant glucose-6-phosphate dehydrogenase (G6PD) gene in a Greek boy who presented with a chronic non-spherocytic haemolytic anaemia. In order to identify the mutation from a small amount of patient material, we adopted an approach which by-passes the need to construct a library by using the polymerase chain reaction. The entire coding region was amplified in eight sections, with genomic DNA as template. The DNA fragments were then cloned in an M13 vector and sequenced. The only difference from the sequence of normal G6PD was a T----G substitution at nucleotide position 648 in exon 7, which predicts a substitution of leucine for phenylalanine at amino acid position 216. This mutation creates a new recognition site for the restriction nuclease BalI. We confirmed the presence of the mutation in the DNA of the patient's mother, who was found to be heterozygous for the new BalI site. This is the first transversion among the point mutations thus far reported in the human G6PD gene.