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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