Bioinformatic analysis of KIT juxtamembrane domain mutations in Syrian GIST patients: jigsaw puzzle completed

Journal of the Egyptian National Cancer Institute

Table 4 Novel variations detected in introns 10 and 11 of the KIT gene in Syrian GIST patients and in silico prediction of their effect on protein structure and function

Genomic change	CDS change	Frequency	fathmm-MKL^a	MutationTaster	AASsites^c
g.74553G > A	c.1774 + 5G > A	2	Pathogenic (0.98)	Disease causing (1)^b	Likely change
g.74557G > A	c.1774 + 9G > A	1	Neutral (0.42)	Polymorphism (0.999)	No change
g.74393G > A	c.1648-29G > A	1	Neutral (0.3)	Polymorphism (0.999)	No change
g.74395G > A	c.1648-27G > A	1	Neutral (0.29)	Polymorphism (0.999)	No change
g.74585delT	c.1774 + 37del	1	NA	Polymorphism (0.999)	NA

^afathmm-MKL: score < 0.5, neutral; score > 0.5, pathogenic; NA, non-applicable. ^bprediction probability, a value close to 1 indicates a high 'security' of the prediction. ^cLikely change, variation changes splicing pattern; no change, variation has no effect on splicing pattern; NA, non-available, test not performed as the tool was not accessible anymore