Missense Substitution In Exon Research Articles

A missense substitution in exon 1 generates the first HLA-DRB1 allele with Valine at residue -17, DRB1*04:354.

A missense nucleotide substitution in codon -17 in the leader peptide results in the novel HLA-DRB1*04:354 allele.

A Novel Homozygous Variant in GJA1 Causing a Hallermann-Streiff/Oculodentodigital Dysplasia Overlapping Phenotype: A Clinical Report

This paper reports the case of a Moroccan girl with a phenotype within the clinical spectrum of both Hallermann-Streiff (HSS, OMIM 234100) and Oculodentodigital Dysplasia (ODDD, OMIM 164200) syndromes. The patient presented with repeated dental abscesses and severe early childhood caries. She had no learning deficit nor psychomotor regression; however, a language delay was noted. She also presented with obstructive sleep apnea syndrome and specific craniofacial features pathognomonic of HSS. Radiographic examination showed enamel and dentin defects, giving a ghost-like tooth appearance. Several clinical features of ODDD overlap those of HSS and may confuse diagnosis, considering that the inheritance of HSS is not described yet. The diagnostic odyssey of this patient ended with the identification by exome sequencing of a novel homozygous alteration in the GJA1 gene. A missense substitution in exon 2 [Chr6(GRCh37): g.121768554C>G NM_000165.4: c.561C>G p.Cys187Trp] was identified by whole-exome sequencing (WES), suggesting a diagnosis of ODDD. This is the first report of a homozygous mutation affecting the second extracellular loop of the CX43 protein.

Neonatal brief resolved unexplained events like episode associated with long QT syndrome and novel missense mutation (Thr1502Ile)

Fetal and neonatal manifestations of long QT syndrome are not well documented except few case reports. We report a neonate presenting with potential brief resolved unexplained events like episode, long QT interval was noted on surface electrocardiogram, and molecular diagnosis revealed a novel heterozygous nonsynonymous missense substitution in exon 17 of the A-kinase anchor protein 9 gene. The proband responded to propranolol at a dose of 1 mg/kg/day.

Is It a Pathogenic ATP7A Variation and Is It Menkes Disease?

This paper is a comment on “Menkes Disease Presenting with Epilepsia Partialis Continua.” While updating the LOVD (Leiden Open Variation Database) ATP7A mutation database (https://grenada.lumc.nl/LOVD2/MD/home.php) I came across a case described by Rizk and colleagues and published in your journal [1]. Rizk and colleagues report a 17-month-old girl who was referred to their hospital with continuous right hand movements which developed suddenly at age of 14 months, regression of milestones, and repetitive episodes of hypothermia. She had hypotonia and constipation. Brain magnetic resonance imaging showed among others cortical and cerebral atrophy. EEG was abnormal and she was diagnosed with epilepsia partialis continua. Magnetic resonance angiography showed relatively tortuous but patent intracranial vessels, with appearance of “hair pin” sign. She had normal hair also with light microscopy. Blood copper and ceruloplasmin levels were normal. The patient was born full term and had normal birth measures. Genetic testing revealed presence of a heterozygous variation, c.1138G>A [p.(Val380Met)], and the authors concluded the diagnosis of Menkes disease (MD) in this patient. Even though the clinical features of this female patient overlap with some of the features observed in Menkes disease patients, she lacks some of the major pathogenic criteria (such as reduced serum copper and ceruloplasmin levels, abnormal hair, hypopigmentation, and cutis laxa) (review in [2]) questioning the clinical diagnosis of Menkes disease, even though female patients may be less severely affected. Furthermore, the ATP7A variation identified is not convincing enough to establish a genetic diagnosis. Firstly, this variation is described at least once in a healthy individual (rs149523862, dbSNP database of short genetic variations, http://www.ncbi.nlm.nih.gov/SNP/), which questions its pathogenicity especially when taking into consideration that MD is a Mendelian disorder. This variation is a missense substitution in exon 4 of ATP7A proximal to but not within the 4th MBD (metal binding domain) of the ATP7A protein. Until now 70 different missense mutations in ATP7A have been described in 94 unrelated patients and none of these mutations were within the first 7 exons of ATP7A encoding the six MBDs [3]. It is generally believed that variations within these regions are more acceptable and do not necessarily lead to MD [3]. Furthermore, two commonly used and publicly available pathogenicity prediction methods, PhD-SNP (http://snps.biofold.org/phd-snp/phd-snp.html) and nsSNP analyser (http://snpanalyzer.uthsc.edu/), categorize this variation as neutral. Secondly, MD is an X-linked recessive disorder and manifesting heterozygotes are rare [4]. It is therefore extremely important to investigate the inheritance of this mutation and to perform X-inactivation studies before evaluating the clinical effect of this variation. In conclusion, the clinical diagnosis of this patient and the pathogenicity of the identified ATP7A variation should be reevaluated.

Identification of a novel TPM1 mutation in a family with left ventricular noncompaction and sudden death

Left ventricular noncompaction (LVNC) is a cardiomyopathy morphologically characterized by 2-layered myocardium, numerous prominent trabeculations, and deep intertrabecular recesses communicating with the left ventricular cavity. The purpose of this study was to investigate patients with LVNC for possible disease causing mutations. We screened 4 genes ( TAZ, LDB3, DTNA and TPM1) in 51 patients with LVNC for mutations by polymerase chain reaction and direct DNA sequencing. A novel missense substitution in exon 1 of TPM1 (c.109A > G: p.Lys37Glu) was identified in three affected members of a family with isolated LVNC. The substitution brings about a change in amino acid charge at a highly conserved residue and could result in aberrant mRNA splicing. This variant was not identified in 200 normal control samples. Pathologic analysis of a right ventricular myocardial specimen from the proband's maternal aunt revealed endocardial and subendocardial fibrosis with prominent elastin deposition, as well as the presence of adipose tissue between muscle layers, pathologic changes that are distinct from those seen in patients with HCM or DCM. Screening of the proband and her mother for variants in other sarcomeric protein-encoding candidate genes, MYH7, MYBPC3, TNNT2, TNNI3, ACTC, MYL2, and MYL3, did not identify any other non-synonymous variants or variants in splice donor–acceptor sequences that were potentially disease causing. We conclude TPM1 is a potential candidate disease-causing gene for isolated LVNC, especially in patients experiencing sudden death.

Mosaic Tetraploidy and Transient Mutations in the GFI1 Gene in a Patient with Severe Chronic Neutropenia.

Severe congenital neutropenia (SCN), also known as Kostmann disease, is a rare disorder characterized by peripheral blood agranulocytosis and maturation arrest of neutrophils within the bone marrow at the promyelocytic stage. Patients usually present with an absolute neutrophil count below 0.2 x 109/L and severe infections, with the typical onset of symptoms during infancy. Most patients respond to treatment with granulocyte colony-stimulating factor, but retain an increased risk for death from sepsis and for development of myelodysplastic syndrome and acute myeloid leukemia (MDS/AML). Several reports have described karyotype abnormalities associated with this syndrome, most typically clonal loss of chromosome 7 or abnormalities of chromosome 21 associated with transformation to MDS/AML. The etiology of these abnormalities and their role in progression to MDS/AML remains unclear. Here we present a case of a 15 year-old boy with SCN, lymphopenia, and persistent tetraploid mosaicism in the bone marrow and in subpopulations of peripheral blood leukocytes. His phenotype, including growth and development, was otherwise normal. The patient's father, who had mild neutropenia and a history of monoclonal gammopathy, also showed a tetraploid subpopulation in his bone marrow. Flow cytometric analysis of the DNA content of CD45+ nucleated cells in the patient's peripheral blood showed that 20% of CD13+ granulocytes, and 15% of CD14+ monocytes were tetraploid. The lifelong persistence of the mosaicism and the similar finding in the patient's father suggest that it represents a congenital propensity towards acquiring tetraploidy. However, cytogenetic evaluation of the patient's skin fibroblasts detected no tetraploidy, indicating failure of the putative tetraploid embryonic cells to contribute to that lineage. The fact that the patient's father also had a population of tetraploid cells in his bone marrow and a history of neutropenia suggests a common underlying genetic cause for both conditions in this kindred.Mutational analysis revealed that the ELA2 gene sequence was normal, but the GFI1 gene exhibited transient, simultaneous appearance of two novel mutations: a missense substitution in exon 1 and a single base change in the promoter region, at a putative binding site for the myeloid-specific transcription factor MZF1. The GFI1 mutations were repeatedly identified in a DNA sample obtained in 2003, but not in 2001, 2002, or 2006 samples. Sequencing of DNA obtained from buccal swabs of the patient and his parents also revealed no GFI1 mutation. The transient appearance may represent the emergence and subsequent loss of a clone of hematopoietic stem or progenitor cells with GFI1 mutations. This hypothesis is supported by a recent report demonstrating that GFI1 mutation results in premature apoptosis of myeloid cells, similar to apoptosis-inducing mutations in the neutrophil elastase gene ELA2. The fact that GFI1 mutations were identified in a DNA sample from one year, but not from others, raises the possibility that GFI1 mutations reported in other neutropenic patients may also be transient. We speculate that an underlying genetic defect, inherited in an autosomal dominant pattern, leads to both disordered mitosis and leukopenia in this kindred.

Variation in genes involved in the RANKL/RANK/OPG bone remodeling pathway are associated with bone mineral density at different skeletal sites in men

In order to assess the contribution of polymorphisms in the RANKL (TNFSF11), RANK (TNFRSF11A) and OPG (TNFRSF11B) genes to variations in bone mineral density (BMD), a population-based cohort with 1,120 extreme low hip BMD cases or extreme high hip BMD controls was genotyped on five SNPs. We further explored the associations between these genetic variations and forearm BMDs by genotyping 266 offspring and 309 available parents from 160 nuclear families. A family-based association test was used. Significantly positive associations were found for A163G polymorphisms in the promoter regions of the OPG gene, a missense substitution in exon 7 (Ala192Val) of the RANK gene and rs9594782 SNP in the 5' UTR of the RANKL gene with BMD in men only. Men with TC/CC genotypes of the rs9594782 SNP had a 2.1 times higher risk of extremely low hip BMD (P = 0.004), and lower whole body BMD (P < 0.001). Subjects with the TC genotype of the Ala192Val polymorphism had a 40% reduced risk of having extremely low hip BMD (P < 0.01), and higher whole body BMD (P < 0.01). Subjects with the GG genotype of the A163G polymorphism had a 70% reduced risk of having extremely low hip BMD (P < 0.05), and higher whole body BMD (P < 0.01). Significant gene-gene interactions were also observed among the OPG, RANK and RANKL genes. Our findings suggest that genetic variation in genes involved in the RANKL/RANK/OPG bone remodeling pathway are strongly associated with BMD at different skeletal sites in adult men, but not in women.

The progesterone receptor Val660→Leu polymorphism and breast cancer risk

BackgroundRecent evidence suggests a role for progesterone in breast cancer development and tumorigenesis. Progesterone exerts its effect on target cells by interacting with its receptor; thus, genetic variations, which might cause alterations in the biological function in the progesterone receptor (PGR), can potentially contribute to an individual's susceptibility to breast cancer. It has been reported that the PROGINS allele, which is in complete linkage disequilibrium with a missense substitution in exon 4 (G/T, valine→leucine, at codon 660), is associated with a decreased risk for breast cancer.MethodsUsing a nested case-control study design within the Nurses' Health Study cohort, we genotyped 1252 cases and 1660 matched controls with the use of the Taqman assay.ResultsWe did not observe any association of breast cancer risk with carrying the G/T (Val660→Leu) polymorphism (odds ratio 1.10, 95% confidence interval 0.93–1.30). In addition, we did not observe an interaction between this allele and menopausal status and family history of breast cancer as reported previously.ConclusionOverall, our study does not support an association between the Val660→Leu PROGINS polymorphism and breast cancer risk.

Polymorphisms in the Low-Density Lipoprotein Receptor–Related Protein 5 (LRP5) Gene Are Associated with Variation in Vertebral Bone Mass, Vertebral Bone Size, and Stature in Whites

Stature, bone size, and bone mass are interrelated traits with high heritability, but the major genes that govern these phenotypes remain unknown. Independent genomewide quantitative-trait locus studies have suggested a locus for bone-mineral density and stature at chromosome 11q12-13, a region harboring the low-density lipoprotein receptor-related protein 5 (LRP5) gene. Mutations in the LRP5 gene were recently implicated in osteoporosis-pseudoglioma and "high-bone-mass" syndromes. To test whether polymorphisms in the LRP5 gene contribute to bone-mass determination in the general population, we studied a cross-sectional cohort of 889 healthy whites of both sexes. Significant associations were found for a missense substitution in exon 9 (c.2047G-->A) with lumbar spine (LS)-bone-mineral content (BMC) (P=.0032), with bone area (P=.0014), and with stature (P=.0062). The associations were observed mainly in adult men, in whom LRP5 polymorphisms accounted for <or=15% of the traits' variances. Results of haplotype analysis of five single-nucleotide polymorphisms in the LRP5 region suggest that additional genetic variation within the locus might also contribute to bone-mass and size determination. To confirm our results, we investigated whether LRP5 haplotypes were associated with 1-year gain in vertebral bone mass and size in 386 prepubertal children. Significant associations were observed for changes in BMC (P=.0348) and bone area (P=.0286) in males but not females, independently supporting our observations of a mostly male-specific effect, as seen in the adults. Together, these results suggest that LRP5 variants significantly contribute to LS-bone-mass and size determination in men by influencing vertebral bone growth during childhood.

PTPN11 mutations in Noonan syndrome type I: detection of recurrent mutations in exons 3 and 13.

We surveyed 16 subjects with the clinical diagnosis of Noonan Syndrome (NS1) from 12 families and their relevant family members for mutations in PTPN11/SHP2 using direct DNA sequencing. We found three different mutations among five families. Two unrelated subjects shared the same de novo missense substitution in exon 13 (S502T); an additional two unrelated families had a mutation in exon 3 (Y63C); and one subject had the amino acid substitution Y62D, also in exon 3. None of the three mutations were present in ethnically matched controls. In the mature protein model, the exon 3 mutants and the exon 13 mutant amino acids cluster at the interface between the N' SH2 domain and the phosphatase catalytic domain. Six of eight subjects with PTPN11/SHP2 mutations had pulmonary valve stenosis while no mutations were identified in those subjects (N = 4) with hypertrophic cardiomyopathy. An additional four subjects with possible Noonan syndrome were evaluated, but no mutations in PTPN11/SHP2 were identified. These results confirm that mutations in PTPN11/SHP2 underlie a common form of Noonan syndrome, and that the disease exhibits both allelic and locus heterogeneity. The observation of recurrent mutations supports the hypothesis that a special class of gain-of-function mutations in SHP2 give rise to Noonan syndrome.