PDGFRa mutations in humans with isolated cleft palate

Isolated cleft palate (CP) is common in humans and has complex genetic etiologies. Many genes have been found to contribute to CP, but the full spectrum of genes remains unknown. PCR-sequencing of the entire coding regions and the 3′ untranslated region (UTR) of the platelet-derived growth factor receptor alpha (PDGFRa) and the microRNA (miR), miR-140 identified seven novel single base-pair substitutions in the PDGFRa in 9/102 patients with CP (8.8%), compared with 5/500 ethnic-matched unaffected controls (1%) (the two-tailed P-value<0.0001). Of these seven, four were missense mutations in the coding regions and three in the 3′UTR. Frequencies of four changes (three in coding, one in 3′UTR) were statistically different from those of controls (P-value<0.05). The c.*34G>A was identified in 1/102 cases and 0/500 controls. This position is conserved in primates and located 10 bp away from a predicted binding site for the miR-140. Luciferase assay revealed that, in the presence of miR-140, the c.*34G>A significantly repressed luciferase activity compared with that of the wild type, suggesting functional significance of this variant. This is the first study providing evidence supporting a role of PDGFRa in human CP.     

<Emphasis Type="Italic">PTPRF</Emphasis> is disrupted in a patient with syndromic amastia

Background  

The presence of mammary glands distinguishes mammals from other organisms. Despite significant advances in defining the signaling pathways responsible for mammary gland development in mice, our understanding of human mammary gland development remains rudimentary. Here, we identified a woman with bilateral amastia, ectodermal dysplasia and unilateral renal agenesis. She was found to have a chromosomal balanced translocation, 46,XX,t(1;20)(p34.1;q13.13). In addition to characterization of her clinical and cytogenetic features, we successfully identified the interrupted gene and studied its consequences.     

Two novel EBP mutations in Conradi-Hünermann-Happle syndrome

Conradi-Hünermann-Happle syndrome, also known as chondrodysplasia punctata type 2 (CDPX2), is an X-linked dominant disorder characterized by skin defects, skeletal and ocular abnormalities. CDPX2 was shown to be caused by mutations in the gene encoding emopamil binding protein (EBP). At least 58 different mutations have been described. Here we present clinical and molecular findings in two unrelated Thai girls with CDPX2. Mutation analysis by PCR-sequencing the entire coding region of EBP successfully revealed two potentially pathogenic, novel mutations, c.616G-->T and c.382delC. This study has expanded the spectrum of the EBP gene mutations causing CDPX2.     

Novel CTSK mutation resulting in an entire exon 2 skipping in a Thai girl with pycnodysostosis

Pycnodysostosis is a rare autosomal recessive skeletal dysplasia characterized by osteosclerosis, short stature, acro‐osteolysis of the distal phalanges, bone fragility and skull deformities. Mutations in the cathepsin K (CTSK) gene, which encodes a lysosomal cysteine protease highly expressed in osteoclasts, have been found to be responsible for the disease. We identified a Thai girl with pycnodysostosis. Her parents were first cousins. Polymerase chain reaction sequencing of the entire coding regions of CTSK of the proband's complementary DNA revealed that the whole exon 2 was skipped. We subsequently amplified exon 2 using genomic DNA, which showed that the patient was homozygous for a c.120G>A mutation. The mutation was located at the last nucleotide of exon 2. Its presence was confirmed by restriction enzyme analysis using BanI. The skipping of exon 2 eliminates the normal start codon. The mutation has never been previously reported, thus the current report expands the CTSK mutational spectrum.     

PTEN c.511C>T nonsense mutation in a BRRS family disrupts a potential exonic splicing enhancer and causes exon skipping

Bannayan-Riley-Ruvalcaba syndrome (BRRS) is an autosomal dominant disorder characterized by macrocephaly, intestinal hamartomatous polyps, lipomas and pigmented macules of the glans penis. We identified a Thai family affected with BRRS. In addition to typical manifestations of BRRS, the proband has a large hepatic AVM which is rarely found in BRRS. The molecular analysis revealed affected members were heterozygous for an exon skipping-associated nonsense mutation c.511C>T in the PTEN gene. The mutation was previously assumed to be deleterious by causing a change to a termination codon, Q171X. We, herein, found that another pathogenic effect was splicing related by disrupting a potential exonic splicing enhancer (ESE) and causing an entire exon 6 skipping. The results prompted us to investigate other reported missense/nonsense mutations in the PTEN gene. We found that they do not colocalize with ESE sites, suggesting that most of their pathogenic effects are not through ESE disruption.     

FGFR2 mutations among Thai children with Crouzon and Apert syndromes

Crouzon and Apert syndromes have been reported to be associated with mutations in Fibroblast Growth Factor Receptor 2 (FGFR2) gene in various ethnic groups, but never in Southeast Asian subjects. Therefore, the authors conducted a study to characterize 11 Thai patients: four with Crouzon syndrome and seven with Apert syndrome. All cases are sporadic. Mean paternal and maternal ages were 38.7 and 28.6 years, respectively. Molecularly, all patients were found to have mutations in the FGFR2 gene. Three mutations (C278F, S347C, S351C) were detected in all Crouzon patients with two having S351C. The seven patients with Apert syndrome have either S252W or P253R mutation. The authors' findings that sporadic cases were associated with advanced paternal age and that they all had mutations in FGFR2 are consistent with previous reports. This is another observation supporting the causative role of FGFR2 mutations in Crouzon and Apert syndromes.     

In vitro Correction of a Novel Splicing Alteration in the BTK Gene by Using Antisense Morpholino Oligonucleotides

A novel sequence variant, c.240+109C>A, in the Bruton’s tyrosine kinase (BTK) gene was identified in a patient with X-linked agammaglobulinemia. This alteration resulted in an incorporation of 106 nucleotides of BTK intron 3 into its mRNA. Administration of the 25-mer antisense morpholino oligonucleotide analog in the patient’s cultured peripheral blood mononuclear cells was able to restore correctly spliced BTK mRNA, a potential treatment for X-linked agammaglobulinemia.     

Primary hyperoxaluria type 1 and brachydactyly mental retardation syndrome caused by a novel mutation in AGXT and a terminal deletion of chromosome 2

Primary hyperoxaluria type 1 (PH1) is an autosomal recessive disorder caused by mutations in the alanine:glyoxylate aminotransferase (AGXT) gene, located on chromosome 2q37. Mutant AGXT leads to excess production and excretion of oxalate, resulting in accumulation of calcium oxalate in the kidney, and progressive loss of renal function. Brachydactyly mental retardation syndrome (BDMR) is an autosomal dominant disorder, caused by haploinsufficiency of histone deacetylase 4 (HDAC4), also on chromosome 2q37. It is characterized by skeletal abnormalities and developmental delay. Here, we report on a girl who had phenotypes of both PH1 and BDMR. PCR-sequencing of the coding regions of AGXT showed a novel missense mutation, c.32C>G (p.Pro11Arg) inherited from her mother. Functional analyses demonstrated that it reduced the enzymatic activity to 31% of the wild-type and redirected some percentage of the enzyme away from the peroxisome. Microsatellite and array-CGH analyses indicated that the proband had a paternal de novo telomeric deletion of chromosome 2q, which included HDAC4. To our knowledge, this is the first report of PH1 and BDMR, with a novel AGXT mutation and a de novo telomeric deletion of chromosome 2q. ? 2012 Wiley Periodicals, Inc.     

ASA E382K disrupts a potential exonic splicing enhancer and causes exon skipping, but missense mutations in ASA are not associated with ESEs

Metachromatic leukodystrophy (MLD) is an autosomal recessive disorder caused by mutations in the arylsulfatase A (ASA) gene. We identified a Thai boy with typical late-infantile MLD and found that he was a compound heterozygote for a novel mutation, g.IVS3-2A>G causing c.679-696del inherited from his father, and a previously reported missense mutation, g.1144G>A causing c.1102-1204del inherited from his mother. The g.1144G>A mutation was located in the middle of exon 7 and previously assumed to be deleterious by causing an amino acid change, E382K. We, herein, found that its actual pathogenic effect was splicing-related by disrupting a potential exonic splicing enhancer (ESE) and causing a complete exon 7 skipping. This is the first missense mutation in the ASA gene that is deleterious from disrupting a potential ESE. The results prompted us to investigate pathogenic effects of other reported missense mutations in the ASA gene. Unlike pathogenic missense mutations in some other genes, those in the ASA gene do not colocalize with ESE sites suggesting that pathogenic effects of majority of them are not splicing-related.