The results of the Sanger test show two patients (VI:1 and VI: 2) in the pedigree are hemizygous for NM_004595: exon9: c.905C>T: p.S302L; the mother and sister (VI:5, V:2) are heterozygous; the father (V:1) and grandmother (paternal side) (II:2) are normal. These results indicate that the rare SNV (NM_004595: exon9: c.905C>T: p.S302L) is co-segregates with the patients’ phenotypes. Since only male carriers showed disease phenotypes, the inheritance pattern of this disease matches XLR.
Clinical details Patient (VI: 1)
The Proband (VI: 1) is a boy, who is 18-years-old born to healthy parents, with a consanguineous marriage, who don’t have any family history of bone deformities and intellectual disability. His birth weight and occipitofrontal circumference (OFC) were 2.20 kg and 34 cm, respectively. He cannot stand and walk, only move by crawling. He has global developmental delay. He has bulging (pigeon-like chest) with no other facial dysmorphic features. The patient exhibited severe dysarthria but did not complain about any visual and auditory problems (Table 1).
Patient (VI: 2)
The patient (VI: 2) is the 8-year-old boy with the complaint of severe pain in bones, hypotonia, regression and lost motor skill in the first two years of life. An EEG at 14 months of age showed generalized slowing and later on, manifested seizures. He had walking problems at an early age. He has multiple a traumatic fracture in tibia, femur and humerus (Table 1).
Patient (VI: 3)
Unfortunately, this patient (VI: 3) died during the study. By the time of his death, he was 10-year-old, and brother of the patient (VI: 1 and VI: 2) and born after an uneventful pregnancy. His weight and OFC were 2.27 kg and 37 cm respectively at birth. He had facial dysmorphic features including a long oval, midface hypoplasia. He had been suffering from respiratory secretions. He had frequent seizures, hypotonia, decreased muscle bulk, and flexion contraction of the large and small joints. He was not able to stand independently and could only move by crawling. He had skeletal problems, including bone fractures of his distal fibula and spine problem. An EEG of the patient manifested slowing background at 14 months of age with no other abnormalities (Table 1).
Genetic and Biochemical Analysis
A mutation, (NM_004595: exon9: c.905C>T: p.S302L), in the SMS gene in the index patient, was identified through the analysis of the data obtained by whole-exome sequencing. This mutation was later confirmed by Sanger sequencing, and we found that this mutation was also present in the carrier mother and a carrier sister (Fig. 2).
The 3D-structure of our protein of interest was already known. We were interested in the mutation of a Serine into a Leucine at position 302. The schematic structures of the WT (left) and the mutant (right) amino acids are shown in figure 3. The backbone is coloured red, which is the same for each amino acid. The side chain is black coloured, which is unique for each amino acid.
Each amino acid is unique because of its specific charge, size, and the hydrophobicity-value. Regarding these properties, the original (WT) residue and the newly introduced mutant residue are often different. Mutation results in the formation of a bigger residue compared to the WT residue. The mutant residue has more hydrophobicity than the WT residue. The effects of the mutation were evaluated based on the contacts made by the mutated residue, structural domains where the residue is located, modifications in this residue and known variants for this residue.
The WT residue forms a hydrogen bond with Isoleucine at position 298. The disparity in size between the WT and mutant residue results in the new residue not being in the correct position to make the same hydrogen bond as the original WT does. The hydrophobicity difference may influence hydrogen bond formation.
The mutation lies within a domain, annotated as PABS in UniProt. The amino acid, which is introduced as a result of mutation, has different properties, which can abolish the domain’s function.
The mutated residue is found in a domain, which is essential for protein activity and interactions with other domains that is also a vital part of the activity. Possible mechanisms for the disruption of normal activity are 1. There is a variation in size of WT and mutant amino acid; 2. The mutant residue has a larger size than the original residue; 3. The WT residue was buried in the protein core, but as the mutant residue is bigger so, it will not fit probably; 4. The hydrophobicity of the WT and the mutant residue is varied; 5. Loss of hydrogen bonds in the protein core will occur because of this mutation, and thus the proper folding will be disturbed.