Skip to main content

Table 3 Damaging variations identified in the affected individuals and selected using different functional prediction tools

From: Family specific genetic predisposition to breast cancer: results from Tunisian whole exome sequenced breast cancer cases

Chromosome-Positiona Locus Gene Reference sequence Variant type Coding change Protein variation Variant Id Frequency Prediction of variant effect Conservation score PhastConsb ClinVar
dbSNP ExAC SIFT Polyphen2 Mutation taster Align-GVGD
Chr1: 120056630 1p12 HSD3B1 NM_000862 Nonsynonymous c.484G > T p.A162S rs997216232 N/A Damaging Probably Damaging Disease causing C65 0.995 N/A
Chr7:117232713 7q31 CFTR NM_000492 Splicing c.2490 + 2T > C rs1057516216 N/A Disease causing 0.998 Likely Pathogenic
Chr8: 27668533 8p21 PBK NM_018492 Nonsynonymous c.714G > C p.W238C rs774498834 8.265e−06 Damaging Probably Damaging Disease causing C65 1 N/A
Chr10:7751028 10p14 ITIH2 NM_002216 Nonsynonymous c.236C > A p.S79Y rs749149620 9.884e−05 Damaging Probably Damaging Disease causing C65 1 N/A
Chr10:99238117 10q24 MMS19 NM_001289403 Nonsynonymous c.292C > T p.R98W rs29001280 0.0015 Damaging Probably Damaging Disease causing C65 1 N/A
Chr13:25671311 13q12 PABPC3 NM_030979 Frameshift deletion c.975_979del p V325 fs rs371130768 8.237e−06 Disease causing 1 N/A
Chr16:4934532 16p13 PPL NM_002705 Nonsynonymous c.4124T > G p.I1375S N/A N/A Damaging Probably Damaging Disease causing C65 1 N/A
Chr16:21011744 16p12 DNAH3 NM_017539 Nonsynonymous c.6223C > T p.P2075S N/A N/A Damaging Probably Damaging Disease causing C65 1 N/A
Chr16:67241867 16q22 LRRC29 NM_001004055 Stopgain c.412C > T p.R138X rs776721799 8.582e−06 Disease causing 0.259 N/A
Chr17:46940292 17q21 CALCOCO2 NM_005831 Stopgain c.1266T > A p.C422X N/A N/A Disease causing 0.999 N/A
Chr19: 53740406 19q13 ZNF677 NM_182609 Frameshift insertion c.1573dupA p.T525 fs rs566714089 0.0038 Disease causing N/A
Chr20: 4766902 20p13 RASSF2 NM_170774 Nonsynonymous c.886C > T p.R296 W rs756486184 8.238e−06 Damaging Probably Damaging Disease causing C65 0.998 N/A
  1. aGRCh37/hg19; b PhastCons values vary between 0 and 1 and reflect the probability that each nucleotide belongs to a conserved element, based on the multiple alignment of genome sequences of 46 different species (the closer the value is to 1, the more probable the nucleotide is conserved)