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Checkpoint kinases (CHK2) - Lab Report Example

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This gene has 27 transcripts (splice variants).In this case, I considered Synonymous variant, a sequence variant where there is no resulting change to the amino acid that is encoded. The amino acid is at position 347. The Transcript has several SNPs but I selected T/C…
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Checkpoint kinases (CHK2)
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Results Variations in the gene This gene has 27 transcripts (splice variants).In this case, I considered Synonymous variant, a sequence variant wherethere is no resulting change to the amino acid that is encoded. The amino acid is at position 347. The Transcript has several SNPs but I selected T/C (rs1805129).The figure below shows variations that exist in the CHK 2 gene.
Figure 1.Variations that exist in the CHK 2 gene
Population Genetics
Basing on the figure below, it is observed that the ancestral nucleotide is T and the new nucleotide is C. Also in the figure we can see the way SNP is distributed in the different populations. In the general population, it is evident that T has 96% while C has 4%.
Figure 2.Summary on population genetics.
The type of changes linked with the SNP.
According to the figure 3,the list indicates several transcripts from the same gene and different SNP effect.The reason to this is as shown in the figure 4 which has all the splice variants(27) of the CHK 2 gene.In the figure 4 ‘‘protein coding” implies that the transcript encodes a CHK 2 protein variant.
Figure 3.Several transcripts with corresponding SNP effects.
Figure 4. The splice variants of the CHK 2 gene
The protein sequence
At position 347 we have Glutamic acid
The reason why we see GAA/GAG yet the SNP was T/C change is that it is a silent mutation whereby GAA and GAG code for glutamic acid.Also the reason why the new C(GAG) is more frequent in some populations is because there was a successful mutation.
Basing on the analysis above, we can see that the SNP resulted to silent mutation. By definition, silent mutation is a type of a point mutation that leads to a codon which codes for different or same amino acid but without any functional change in that particular protein. Hence, it does not cause change in the sequence of amino acid, thus, the protein will remain functional. In this regard, they are taken to be evolutionarily neutral. In relation to this, the CHK2 SNP (T/C) is considered to be silent mutation because the sequence of the protein which is GAA/GAG remains unchanged. Therefore, its function remains the same. It can therefore influence splicing because the nucleotides sequence has been altered.
While most of the RNA transcripts from protein encoding genes of the human genome are related to physiological splicing, pathological splicing has been found in cancer tissue (Berge et al, 2010). The Chk2 is known to be a multi-organ susceptible gene that provides a barrier to tumorigenesis to maintain a genomic stability, and this gene has found mutated in both hereditary and somatic cancer. Despite the fact that other genes’ alternative splice forms have been found to have a negative impact on the wild type molecules, the CHK2 splice protein variants function is still not clear(Berge et al, 2010).For instance, the mRNA splice variants for Chk2 gene were identified in human breast carcinomas. In this case, the variants CHK2Delta 11 and Chk2isol were found to be inactive (Berge et al, 2010)
Reference
Berge EO, Staalesen V, Straume AH, Lillehaug JR, Lønning PE. Biochim Biophys Acta. 2010 Mar; 1803(3):386-95. Epub 2010 Jan 15 Read More
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