Polymorphisms in the thymidylate synthase promoter and the DNA repair genes XRCC1 and XPD in a Brazilian population

Polymorphisms in genes responsible for maintaining genomic integrity are potential modifiers of disease risk. Since considerable interindividual and interethnic variation in DNA repair capacity has been associated with polymorphic alleles, we evaluated the frequency of the 2R/3R variants in the TS promoter, Arg194Trp and Arg399Gln in the XRCC1 gene, and Asp312Asn and Lys751Gln in the XPD gene in 364 healthy individuals from a Brazilian population separated by ethnicity (European ancestry and African ancestry). The genotypes were determined by PCR (TS) or by PCR-RFLP (XRCC1 and XPD). The frequency of the TS 3R allele was 0.56 for whites and 0.51 for nonwhites. In the case of the XRCC1 MspI polymorphism, the allele frequencies were 0.09 for 194Trp in both nonwhites and whites and 0.27 and 0.28 for 399Gln in nonwhites and whites, respectively. For the XPD 312Asn allele, we found a frequency of 0.25 in white individuals, which was significantly different (P = 0.025) from that seen in nonwhites (0.15). Similarly, the 751Gln polymorphic allele of the XPD gene was significantly more frequent (P < 0.002) in whites (0.30) than in nonwhites (0.20). The genotype frequencies were within Hardy-Weinberg equilibrium. We concluded that the genotype and allele frequencies of XPD gene polymorphism differed between white and nonwhite Brazilians, and that the frequencies of the XPD 312Asn and XRCC1 399Gln alleles in this Brazilian population showed ethnic variability when compared with those observed in other populations.     

DNA repair gene XRCC1 and XPD polymorphisms and the risk of idiopathic azoospermia in a Chinese population

Genetic polymorphisms in DNA repair genes may influence individual variation in DNA repair capacity and further influence the risk of developing cancer. However, little information is available on these polymorphisms in infertility. To investigate whether polymorphisms in DNA repair genes, X-ray repair cross-complementing group 1 (XRCC1) and xeroderma pigmentosum group D (XPD), alone or in combination, are associated with the risk of developing idiopathic azoospermia, the genotype and allele frequencies of three observed polymorphisms (XRCC1 Arg194Trp and Arg399Gln, and XPD Lys751Gln) were examined by polymerase chain reaction-restriction fragment length polymorphism based on a Chinese population consisting of 171 idiopathic azoospermia patients and 247 normal-spermatogenesis fertile controls. Associations between the polymorphisms and the idiopathic azoospermia risk were estimated by logistic regression, and the Statistical analysis system was used to test the gene-gene joint effects. All observed polymorphisms were in agreement with Hardy-Weinberg equilibrium. The XPD 751Gln allele seemed to be a risk allele for azoospermia, with a frequency of 11.40% in the cases and 5.67% in the controls (p=0.004). Compared with the Lys/Lys genotype, the XPD 751 Lys/ increased 5.100- or 3.064-fold, respectively, when combined with the XRCC1 194 Arg/Arg or 399 Arg/Arg genotype. In conclusion, our study provided the first evidence that the XPD and XRCC1 polymorphisms contributed to the risk of developing idiopathic azoospermia in a selected Chinese population.     

Schuurs‐Hoeijmakers syndrome in a patient from India

Schuurs‐Hoeijmakers syndrome (SHMS), or Autosomal Dominant Mental Retardation Syndrome type 17 (MRD17) is a rare form of intellectual disability with distinct facial features. A recurrent de novo heterozygous c.607C>T, p.Arg203Trp mutation in the PACS1 gene accounts for all reported cases except for one patient with a de novo heterozygous c.608G>A, p.Arg203Trp mutation. Ethnic background is known to affect the clinical manifestation of dysmorphic syndromes. Here we describe the first Indian patient with Schuurs‐Hoeijmakers syndrome (SHMS) with a de novo heterozygous NM_018026.3 (PACS1):c.607C>T (p.Arg203Trp) variant. He is the only child with SHMS with a cleft lip. Thus our report expands the phenotypic spectrum of SHMS and establishes its occurrence across populations.     

PIK3R1 mutations in SHORT syndrome

SHORT syndrome (OMIM 269880) is a rare autosomal‐dominant disorder characterized by short stature, hyperextensibility of joints, hernias, ocular depression, ophthalmic anomalies (Rieger anomaly, posterior embryotoxon, glaucoma), teething delay, partial lipodystrophy, insulin resistance and facial dysmorphic signs. Heterozygous mutations in PIK3R1 were recently identified in 14 families with SHORT syndrome. Eight of these families had a recurrent missense mutation (c.1945C>T; p.Arg649Trp). We report on two unrelated patients with typical clinical features of SHORT syndrome and additional problems such as pulmonary stenosis and ectopic kidney. Analysis of PIK3R1 revealed the mutation c.1945C>T; p.Arg649Trp de novo in both patients. These two patients not only provide additional evidence that PIK3R1 mutations cause SHORT syndrome, but also broaden the clinical spectrum of this syndrome and further confirm that the amino acid exchange c.1945C>T; p.Arg649Trp is a hotspot mutation in this gene.     

Identification and functional analysis of an ADAMTSL1 variant associated with a complex phenotype including congenital glaucoma,craniofacial, and other systemic features in a three‐generation human pedigree

Developmental glaucoma can occur as an isolated or syndromic condition and is genetically heterogeneous. We describe a three‐generation family affected with developmental glaucoma, myopia, and/or retinal defects associated with variable craniofacial/dental, auditory, brain, renal, and limb anomalies. Whole‐exome sequencing identified a heterozygous c.124T> C, p.(Trp42Arg) allele in ADAMTSL1; cosegregation analysis confirmed the presence of this allele in four affected family members. The mutation affects a highly conserved residue and is strongly predicted to have a deleterious effect on protein function. Trp42 is normally modified by protein C‐mannosylation, an unusual post‐translational modification. Comparison of ADAMTSL1‐WT (also known as punctin‐1) and ADAMTSL1‐p.Trp42Arg in vitro demonstrated that the latter was not secreted from transfected cells but retained intracellularly. Moreover, ADAMTSL1‐p.Trp42Arg reduced secretion of cotransfected wild‐type ADAMTSL1, suggesting a dominant negative effect for this mutation. These data imply a multisystem role for ADAMTSL1 and present the first disease‐associated variant affecting a C‐mannosylation motif.     

The genetic profile of dysferlinopathy in a cohort of 209 cases: Genotype–phenotype relationship and a hotspot on the inner DysF domain

Dysferlinopathy is a group of autosomal recessive muscular dystrophies caused by variants in the dysferlin gene (DYSF), with variable proximal and distal muscle involvement. We performed DYSF gene analyses of 200 cases suspected of having dysferlinopathy (Cohort 1), and identified diagnostic variants in 129/200 cases, including 19 novel variants. To achieve a comprehensive genetic profile of dysferlinopathy, we analyzed the variant data from 209 affected cases from unrelated 209 families, including 80 previously diagnosed and 129 newly diagnosed cases (Cohort 2). Among the 90 types of variants identified in 209 cases, the NM_003494.3: c.2997G>T; p.Trp999Cys, was the most frequent (96/420; 22.9%), followed by c.1566C>G; p.Tyr522* (45/420; 10.7%) on an allele base. p.Trp999Cys was found in 70/209 cases (33.5%), including 20/104 cases (19.2%) with the Miyoshi muscular phenotype and 43/82 cases (52.4%) with the limb‐girdle phenotype. In the analysis of missense variants, p.Trp992Arg, p.Trp999Arg, p.Trp999Cys, p.Ser1000Phe, p.Arg1040Trp, and p.Arg1046His were located in the inner DysF domain, representing in 113/160 missense variants (70.6%). This large cohort highlighted the frequent missense variants located in the inner DysF domain as a hotspot for missense variants among our cohort of 209 cases (>95%, Japanese) and hinted at their potential as targets for future therapeutic strategies.     

Analysis of ERCC2/XPD functional polymorphisms in systemic lupus erythematosus

Sunlight/ultraviolet (UV) irradiation has been recognized as an important risk factor for developing systemic lupus erythematosus (SLE). However, the interpretation of genetic variations involved in UV‐light sensitivity is largely unknown. Recent studies indicated that two genetic variations of ERCC2/XPD gene (rs1799793 in exon 10 and rs13181 in exon 23) have been found to exert negative influences on nucleotide excision repair system. To analyse the possible contribution of the ERCC2/XPD functional single nucleotide polymorphisms in genetic susceptibility to SLE, the rs13181 and rs1799793 SNPs in ERCC2/XPD were genotyped by polymerase chain reaction followed by restriction fragment length polymorphism analysis. Association was studied by case–control analyses using samples from 172 SLE patients and 160 healthy controls. Haplotype analysis was performed to detect the association with genetic predisposition to SLE and the clinical features. Although these two functional genetic variations are linked to several immune dysfunction‐induced diseases, no statistically significant differences in allele or genotype frequencies were observed between SLE patients and controls. Haplotype analysis showed that none of ERCC2/XPD haplotypes was associated with the incidence of SLE disease, nor the preference of clinical features. In conclusion, the ERCC2/XPD functional polymorphisms analysed in this study showed no association in genetic susceptibility to SLE.