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Table 1 Truncating variants

From: Prevalence of PALB2 mutations in Australian familial breast cancer cases and controls

Exon Nucleotide changea Predicted protein changea dbSNP ID First reported HAPS cases
(n = 997)b
FCC-ViP cases
(n = 999)b
Controls (n = 1998)b CADD scaled C score
3 c.172_175delTTGT p.Gln60Argfs*7 . Jones (2009) - 1 - 19.0
3 c.196C > T p.Gln66* rs180177083 Casadei (2011) [29] 2 - - 35.0
4 c.522_523delAA p.Arg175Thrfs*9 . - - 1 - 23.2
4 c.577dupA p.Thr193Asnfs*2 . - 1 - - 11.6
4 c.693dupA p.Gly232Argfs*3 . - 1 - - 11.2
4 c.758dupT p.Ser254Ilefs*3 . Zheng (2012) [40] 1 1 - 16.2
4 c.860dupT p.Ser288Lysfs*15 . - 1 - - 17.6
5 c.1947dupA p.Glu650Argfs*13 . Teo (2013) [8] - 1 - 24.1
5 c.1947_1966dup p.Pro656Glnfs*11 . - 1 - - 13.0
5 c.2386G > T p.Gly796* rs180177112 Rahman (2007) [3] - 1 - 32.0
5 c.2391delA p.Gln797Hisfs*54 . Wong-Brown (2013) 1 - - 23.5
9 c.2966_2967insCAACAAGT p.Glu990Asnfs*3 . - - - 1 20.7
9 c.2982dupT p.Ala995Cysfs*16 rs180177127 Rahman (2007) [3] 1 - - 31.0
10 c.3113G > A p.Trp1038*c rs180177132 Rahman (2007) [3] 2 5 1 42.0
11 c.3116delA p.Asn1039Ilefs*2 rs180177133 Reid (2007) [2]; Rahman (2007) [3] - 1 1 40.0
12 c.3256C > T p.Arg1086* . Jones (2009) - 1 - 40.0
13 c.3362delG p.Gly1121Valfs*3 . Blanco (2013) [27] - 1 1 22.1
13 c.3507_3508del p.His1170Phefs*19 . Antoniou (2014) [5] 1 - - 40.0
13 c.3549C > G p.Tyr1183* rs118203998 Reid (2007) [2] 1 - - 37.0
  1. HAPS Hunter Area Pathology Service, FCC Familial Cancer Centre, ViP Variants in Practice
  2. aVariant positions are reported in reference to NCBI RefSeq NM_024675.3 (mRNA) and NP_078951.2 (protein)
  3. bNumber of individuals carrying the variant
  4. cc.3113G > A produces three different PALB2 mRNA sequences: complete deletion of exon 10 (117 bp); use of an alternative splice site within exon 10, and deletion of 31 bp; and an immediate stop at codon 1038 [29]