1Department of Radiation Oncology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
2LabGenomics Clinical Research Institute, LabGenomics, Seongnam, Korea
3Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
4Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
Copyright © 2016 by the Korean Cancer Association
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SIFT, Sorting Intolerant From Tolerant; PolyPhen-2, Polymorphism Phenotyping ver. 2; L, Leiden Open Variation Database (LOVD; http://www.lovd.nl/3.0/); C, ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); T, 1000Genome (http://www.1000genomes.org/); V, Exome Variant Server (http://evs.gs.washington.edu/EVS/); E, Exome Aggregation Consortium (EXAC; http://exac.broadinstitute.org/); D, dbSNP (http://www.ncbi.nlm.nih.gov/SNP/); H, Human Genome Mutation Database (HGMD; http://www.hgmd.cf.ac.uk/ac/).
Location | Nucleotide change | Effect on protein | Allele frequency |
SIFT result | SIFT score | PolyPhen-2 result | PolyPhen-2 score | dbSNP | Reference database | |
---|---|---|---|---|---|---|---|---|---|---|
Patient | Control | |||||||||
Coding region | ||||||||||
Exon 5 | c.430G>A | p.A144T | 3/470 | - | Tolerated | 0.55 | Probably damaging | 0.999 | rs116952709 | L, C, T, V, E |
Exon 6 | c.587A>G | p.N196S | 2/470 | - | Tolerated | 0.74 | Benign | 0.030 | - | L, C, E |
Exon 7 | c.787C>T | p.L263F | 2/470 | 0/100 | Damaging | 0.01 | Probably damaging | 1.000 | - | - |
Exon 8 | c.1018C>T | p.L340F | 1/470 | 0/100 | Damaging | 0.04 | Probably damaging | 0.981 | - | E |
Exon 10 | c.1421T>C | p.L474P | 1/470 | 0/100 | Damaging | 0.02 | Probably damaging | 0.996 | - | - |
Exon 10 | c.1442G>A | p.G481D | 2/470 | - | Tolerated | 0.12 | Probably damaging | 1.000 | - | C, E |
Exon 18 | c.2543G>A | p.R848H | 1/470 | - | Damaging | 0.00 | Probably damaging | 1.000 | rs374334794 | C, T, V |
Exon 19 | c.2637A>G | - | 118/470 | - | - | - | - | - | rs4986765 | L, D, T, V, E |
Exon 19 | c.2755T>C | p.S919P | 119/470 | - | Tolerated | 0.28 | Benign | 0.001 | rs4986764 | L, C, D, T, V, E |
Exon 19 | c.2830C>G | p.Q944E | 2/470 | - | Tolerated | 1.00 | Possibly damaging | 0.634 | rs140233356 | L, H, C, D, T, E |
Exon 19 | c.2854A>G | p.I952V | 2/470 | - | Tolerated | 0.68 | Benign | 0.001 | rs200239986 | D, T, E |
Exon 20 | c.3411T>C | - | 134/470 | - | - | - | - | - | rs4986763 | L, D, T, V, E |
Non-coding region | ||||||||||
Intron 5 | c.380-17T>A | - | 1/470 | - | - | - | - | - | - | E |
Intron 6 | c.508-31C>G | - | 131/470 | - | - | - | - | - | rs4988344 | L, D, V, E |
Intron 7 | c.918+15T>A | - | 11/470 | - | - | - | - | - | rs117820198 | L, C, D, E |
Intron 8 | c.1140+91dupT | - | 133/470 | - | - | - | - | - | rs11390869 | - |
Intron 12 | c.1629-48T>C | - | 1/470 | - | - | - | - | - | - | - |
Intron 13 | c.1795-47G>C | - | 114/470 | - | - | - | - | - | rs4988351 | L, D, V, E |
Intron 14 | c.1936-70C>A | - | 1/470 | - | - | - | - | - | - | C |
Intron 15 | c.2257+19A>C | - | 13/470 | - | - | - | - | - | rs77851913 | L, D, V, E |
Patient No. | Variant | Age at diagnosis | Type of cancer | Family history of cancer |
---|---|---|---|---|
1 | c.787C>T | 25 | Bilateral breast cancer | Hepatic cancer (grandfather), lung cancer (maternal grandfather) |
2 | c.787C>T | 42 | Breast cancer | Lung cancer (maternal uncle) |
3 | c.1018C>T | 46 | Breast cancer | Breast cancer (maternal cousin, diagnosed in her 50s), pancreas cancer (mother), stomach cancer (father) |
4 | c.1421T>C | 33 | Breast cancer | - |
5 | c.2543G>A | 54 | Bilateral breast cancer and ovarian cancer | Breast cancer (aunt, diagnosed in her 60s), leukemia (maternal aunt) |
SIFT, Sorting Intolerant From Tolerant; PolyPhen-2, Polymorphism Phenotyping ver. 2; L, Leiden Open Variation Database (LOVD;