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

Breast Cancer Research

Table 1 Truncating variants

Exon	Nucleotide change^a	Predicted protein change^a	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

HAPS Hunter Area Pathology Service, FCC Familial Cancer Centre, ViP Variants in Practice
^aVariant positions are reported in reference to NCBI RefSeq NM_024675.3 (mRNA) and NP_078951.2 (protein)
^bNumber of individuals carrying the variant
^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]

ISSN: 1465-542X