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Table 3 Missense variants

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

Exon Nucleotide changea Protein changea dbSNP ID First reported 1000 G MAFb NHBLI GO ESP MAFc ExACd HAPS cases
(n = 997)e
FCC-ViP cases (n = 999)e Controls
(n = 1998)e
CADD scaled
C score
Condel PolyPhen2 SIFT
1 c.11C > T p.Pro4Leu rs45619737 Rahman (2007) [3] . 0.00038 0.0000999 1 1 1 12.9 Deleterious Probably damaging Tolerated
2 c.53A > G p.Lys18Arg rs138789658 Tischkowitz (2008) 0.0032 0.00523 0.0000552 - - 1 18.0 Deleterious Possibly damaging Deleterious
2 c.94C > G p.Leu32Val rs151316635 Teo (2013) [8] . 0.00023 0.0000184 - 1 1 16.3 Deleterious Possibly damaging Deleterious
3 c.194C > T p.Pro65Leu rs62625272 Adank (2011) [26] . 0.00015 0.00006 - - 1 4.6 Neutral Benign Tolerated
4 c.232G > A p.Val78Ile . Tischkowitz (2012) [39] . . 0.000325   2   0.4 Neutral Benign Tolerated
4 c.298C > T p.Leu100Phe rs61756147 Wong (2011) [9] 0.0005 0.00023 0.000037 - - 2 10.3 Neutral Probably damaging Tolerated
4 c.344G > T p.Gly115Val rs145598272 Foulkes (2007) [34] . 0.00015 0.0000921 1 - 1 6.5 Neutral Benign Tolerated
4 c.353 T > C p.Ile118Thr . - . 0.00008 0.000037 - - 1 5.4 Neutral Benign Tolerated
4 c.400G > A p.Asp134Asn rs139555085 Zheng (2011) 0.0005 0.00184 0    1 4.8 Neutral Benign Tolerated
4 c.508A > G p.Arg170Gly . - . . . - - 1 4.4 Neutral Benign Tolerated
4 c.557A > T p.Asn186Ile . - . . . - - 1 13.1 Deleterious Probably damaging Deleterious
4 c.571C > G p.Pro191Ala . - . . . - - 1 9.4 Neutral Probably damaging Tolerated
4 c.629C > T p.Pro210Leu rs57605939 Rahman (2007) [3] 0.0174 0.02216 0.0000736 1 1 2 10.6 Deleterious Probably damaging Tolerated
4 c.899C > T p.Thr300Ile . Ding (2011) . . 0 1 - - 15.1 Deleterious Probably damaging Tolerated
4 c.656A > G p.Asp219Gly rs45594034 Rahman (2007) [3] . 0.00015 0.000221   1   1.8 Neutral Benign Tolerated
4 c.740C > G p.Thr247Arg . . . . .   1   15.5 Deleterious Probably damaging Tolerated
4 c.925A > G p.Ile309Val rs3809683 Rahman (2007) [3] 0.0087 0.00970 0.0000184 4 (1) - - 0.5 Neutral Benign Tolerated
4 c.1010 T > C p.Leu337Ser rs45494092 Rahman (2007) [3] 0.0133 0.01424 0.0197 44 (1) 44 93 (1) 8.9 Deleterious Probably damaging Tolerated
4 c.1085 T > C p.Leu362Pro . - . . . 1 - - 14.4 Deleterious Probably damaging Tolerated
4 c.1145G > T p.Ser382Ile . Tischkowitz (2012) [39] . . 0.0000184 - 1 - 15.2 Deleterious Possibly_damaging Deleterious
4 c.1189A > T p.Thr397Ser . Rahman (2007) [3] . 0.00008 0.0000184 - 1 1 22.9 Deleterious Possibly damaging Deleterious
4 c.1250C > A p.Ser417Tyr rs45510998 Rahman (2007) . . 0.000203 - - 1 20.6 Deleterious Probably damaging Deleterious
4 c.1478C > T p.Pro493Leu . - . . 0.0000184 - - 1 12.4 Neutral Benign Tolerated
4 c.1492G > T p.Asp498Tyr rs75023630 Phuah (2013) [38] 0.0014 . 0 - - 1 16.2 Deleterious Benign Deleterious
4 c.1544A > G p.Lys515Arg . Tischkowitz (2012) [39] . . 0.000037 - 1 - 16.2 Deleterious Possibly damaging Tolerated
4 c.1610C > T p.Ser537Leu rs142103232 - . 0.00015 0.000166 - 1 - 11.2 Neutral Possibly damaging Tolerated
4 c.1676A > G p.Gln559Arg rs152451 Rahman (2007) [3] 0.1465 0.13483 0.0961 216 (9) 182 (11) 335 (10) 0.0 Neutral Benign Tolerated
5 c.1699C > T p.His567Tyr . Tischkowitz (2012) [39] . 0.00008 0.000094 - - 1 0.9 Neutral Benign Tolerated
5 c.1931G > A p.Gly644Glu . - . . . - - 1 16.0 Deleterious Probably damaging Deleterious
5 c.2014G > C p.Glu672Gln rs45532440 Rahman (2007) [3] 0.0142 0.02324 0.0278 64 (1) 68 (4) 123 (1) 11.4 Neutral Possibly damaging Tolerated
5 c.2106A > G p.Ile702Met . - . . 0.0000184 1 - - 11.1 Neutral Probably damaging Tolerated
5 c.2135C > T p.Ala712Val rs141458731 Dansonka-Meiszkowska (2010) 0.0014 0.00062 0.00039 - - 1 12.2 Neutral Benign Tolerated
5 c.2200A > T p.Thr734Ser rs45543843 Rahman (2007) [3] . . 0.0000368 - - 3 25.3 Deleterious Possibly damaging Deleterious
5 c.2228A > G p.Tyr743Cys rs141749524 - 0.0009 . 0.0000184 1 - - 8.5 Neutral Benign Tolerated
5 c.2289G > C p.Leu763Phe . Phuah (2013) [38] . . 0 2 - - 15.5 Neutral Probably damaging Tolerated
5 c.2360C > T p.Thr787Ile rs201042302 - 0.0005 . 0 - 1 - 9.7 Neutral Probably damaging Tolerated
5 c.2417C > T p.Pro806Leu rs45464991 Rahman (2007) [3] . 0.00008 0.000037 - 1 1 0.5 Neutral Benign Tolerated
7 c.2590C > T p.Pro864Ser rs45568339 Rahman (2007) [3] 0.0018 0.00239 0.00396 6 10 19 12.0 Neutral Benign Tolerated
7 c.2606C > G p.Ser869Cys . . . . 0.0000184   1   19.9 Deleterious Probably damaging Deleterious
7 c.2674G > A p.Glu892Lys rs45476495 Rahman (2007) [3] . 0.00008 0.000092 1 2 - 20.8 Deleterious Possibly damaging Deleterious
8 c.2755G > A p.Val919Ile . - . . . - - 1 15.7 Neutral Benign Tolerated
8 c.2794G > A p.Val932Met rs45624036 Rahman (2007) [3] 0.0009 0.00431 0.00869 15 8 23 18.3 Deleterious Probably damaging Tolerated
8 c.2816 T > G p.Leu939Trp rs45478192 Rahman (2007) [3] 0.0009 0.00154 0.0015 2 3 (1) 8 20.9 Deleterious Probably damaging Deleterious
9 c.2993G > A p.Gly998Glu rs45551636 Rahman (2007) [3] 0.0105 0.01785 0.0213 42 46 (2) 92 (1) 22.7 Deleterious Probably damaging Deleterious
10 c.3054G > C p.Glu1018Asp rs183489969 Tischkowitz (2012) [39] 0.0009 . 0 1 - 1 16.4 Deleterious Possibly damaging Deleterious
10 c.3106G > C p.Val1036Leu . - . . 0.000037 - 1 - 13.3 Neutral Benign Tolerated
11 c.3128G > C p.Gly1043Ala . Hellebrand (2011) [36] 0.0009 . 0.000037 1 - - 20.9 Deleterious Probably damaging Deleterious
11 c.3146 T > C p.Met1049Thr rs138273800 - . 0.00008 . - 1 - 18.0 Deleterious Probably damaging Deleterious
12 c.3307G > A p.Val1103Met rs201657283 Casadei (2011) [29] . 0.00015 0.0000184 - 1 - 13.0 Neutral Benign Tolerated
13 c.3366C > A p.Asp1122Glu . . . . . -   1 16.0 Neutral Possibly damaging Tolerated
13 c.3367G > A p.Val1123Met    . . . - 1 - 18.7 Deleterious Probably damaging Deleterious
13 c.3428 T > A p.Leu1143His rs62625284 Balia (2010) . 0.00008 0.00031 2 - - 20.0 Deleterious Possibly damaging Tolerated
13 c.3448C > T p.Leu1150Phe    . . . - 1 - 15.5 Deleterious Possibly damaging Deleterious
13 c.3449 T > G p.Leu1150Arg rs45566737   . . 0.0000368 - 1 - 18.2 Deleterious Possibly damaging Deleterious
  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. bMinor allele frequency (MAF) reported in the 1000 Genomes (1000 G) cohort Phase 1
  4. cMAF reported in the Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP) [46] (data release ESP6500SI-V2)
  5. dMAF reported in ExAC [45] from non-Finnish Europeans, excluding individuals in the database who were part of The Cancer Genome Atlas and therefore known to have had cancer
  6. eNumber of individuals carrying the variant. Where applicable, the number of homozygous carriers is indicated in parentheses