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Table 2 Predicting the effects of PALB2 missense variants on protein function using three in silico methods.

From: Prevalence of PALB2 mutations in Australasian multiple-case breast cancer families

Nucleotide change Protein change Carrier frequency (%) SIFT a Align GVGD b Polyphen c
c.90G>T p.Lys30Asn 1 (0.1) Affect protein function; P = 0.04 Class C0 Probably damaging 0.999
c.94C>G p.Leu32Val 1 (0.1) Tolerated; P = 0.37 Class C0 Probably damaging 1.000
c.596A>G p.Asp219Gly 1 (0.1) Tolerated; P = 0.65 Class C0 Benign 0.000
c.956C>A p.Ser319Tyr 1 (0.1) Tolerated; P = 0.91 Class C0 Possibly damaging 0.589
c.1010T>C p.Leu337Ser 25 (3.3) Tolerated; P = 0.59 Class C0 Benign 0.291
c.1475G>T p.Gly492Val 1 (0.1) Tolerated; P = 0.17 Class C0 Benign 0.161
c.1676A>G p.Gln559Arg 72 (9.6) Tolerated; P = 0.57 Class C0 Benign 0.000
c.2014G>C p.Glu672Gln 51 (6.8) Tolerated; P = 0.48 Class C0 Benign 0.225
c.2590C>T p.Pro864Ser 1 (0.1) Tolerated; P = 0.68 Class C0 Possibly damaging 0.578
c.2993G>A * p.Gly998Glu 17 (0.9) Affect protein function; p = 0.00 Class C65 Probably damaging 1.000
  1. *Predicted to affect protein function by all three programs. aKumar et al.(2009) [24]; Ng et al (2003) [25]. bTavtigian et al. (2006) [27]; Mathe et al. (2006) [28]; Tavtigian et al. (2008) [29]. cAdzhubei et al. (2010) [31].