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Table 3 CRAVAT functional analysis outcome of the two variants of prime interest identified in the 11 family members

From: Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach

HUGO gene symbol HGVS description of variant HGMD tag Sequence ontology Driver genes Target Occurrences in COSMIC by primary sites (gene mutated)
MSH2 c.2732T>A NA Missense variant TSG NA Cervix(1), large intestine (106), autonomic ganglia (2), central nervous system (2), liver(1), small intestine (1), haematopoietic and lymphoid tissue (7), endometrium (18), urinary tract (1), lung (14), breast (7), skin (4), stomach (1), esophagus (1), ovary (4), NS (2), prostate (2), kidney (6), pancreas (1)
BRCA1 c.2955delC DM Frameshift deletion TSG PARP inhibitor Cervix (1), large intestine (66), stomach (8), central nervous system (2), pancreas (1), meninges (1), haematopoietic and lymphoid tissue (3), endometrium (23), urinary tract (5), lung (42), liver (5), skin (6), oesophagus (4), ovary (39), NS (2); prostate (2), kidney (5), breast (33)
  1. Source: CRAVAT tool. In the case of MSH2, cancer driver analyses were also performed, selecting “colon” as the tissue type of interest. A driver score of 0.27 was obtained (a driver score close to zero means an increased probability of the mutation being a cancer driver)
  2. TSG tumor suppressor gene, NA not available