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Table 2 Functional and common non-synonymous form of single nucleotide polymorphisms (nsSNPs) from the breast tissue-expressed carcinogenesis-related genes.

From: Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: Potential breast cancer risk alleles and their distribution across human populations

Genea

Accession

number

SNP IDb

Amino acid

changec

Codond

Damaging

allele

Damaging

amino acide

PolyPhen

prediction

Pathwayf

ACY1

NM_000666.1

rs2229152

R386C

cgt/tgt

t

C

Probably damaging

IM

ADD1

NM_014189.2

rs4961

G460W

ggg/tgg

t

W

Probably damaging

IM

ADD1

NM_014189.2

rs4962

N541I

aat/att

t

I

Probably damaging

IM

ADD1

NM_014189.2

rs4971

Y270N

tat/aat

a

N

Probably damaging

IM

ADM

NM_001124.1

rs5005

S50R

agc/agg

g

R

Possibly damaging

AN

ADRB2

NM_000024.3

rs1042713

G16R

gga/aga

a

R

Possibly damaging

BE, IM

ALDH2

NM_000690.2

rs671

E504K

gaa/aaa

a

K

Possibly damaging

IM, PH

APOE

NM_000041.1

rs429358

C130R

tgc/cgc

c

R

Probably damaging

IM

AXIN2

NM_004655.1

rs2240308

P50S

cct/tct

t

S

Probably damaging

DE

C2

NM_000063.3

rs4151648

R734C

cgc/tgc

t

C

Possibly damaging

IM

CD2

NM_001767.2

rs699738

H266Q

cac/caa

a

Q

Probably damaging

AN, IM, MET

CDH12

NM_004061.2

rs4371716

V68M

gtg/atg

g

V

Probably damaging

IM

CHGA

NM_001275.2

rs729940

R399W

cgg/tgg

t

W

Probably damaging

IM

CHGA

NM_001275.2

rs9658667

G382S

ggc/agc

a

S

Possibly damaging

IM

CLU

NM_001831.1

rs9331936

N317H

aac/cac

c

H

Possibly damaging

IM

CSF1

NM_000757.3

rs2229165

G438R

ggg/agg

a

R

Probably damaging

IM

CSF3R

NM_000760.2

rs3917973

M231T

atg/acg

c

T

Probably damaging

IM

CSF3R

NM_000760.2

rs3917974

Q346R

cag/cgg

g

R

Possibly damaging

IM

CSF3R

NM_000760.2

rs3917991

D510H

gac/cac

c

H

Possibly damaging

IM

CYBA

NM_000101.1

rs4673

Y72H

tac/cac

c

H

Possibly damaging

IM

CYP11B1

NM_000497.2

rs4541

A386V

gcg/gtg

c

A

Possibly damaging

PH

CYP11B1

NM_000497.2

rs5287

M160I

atg/atc

c

I

Possibly damaging

PH

CYP11B1

NM_000497.2

rs5294

Y439H

tac/cac

t

Y

Probably damaging

PH

CYP11B1

NM_000497.2

rs5312

E383V

gag/gtg

t

V

Probably damaging

PH

CYP1B1

NM_000104.2

rs1800440

N453S

aac/agc

g

S

Possibly damaging

IM, PH

CYP2A6

NM_000762.4

rs1801272

L160H

ctc/cac

a

H

Probably damaging

IM, PH

CYP2B6

NM_000767.3

rs2279343

K262R

aag/agg

a

K

Possibly damaging

PH

CYP2C9

NM_000771.2

rs1799853

R144C

cgt/tgt

t

C

Probably damaging

IM, PH

DAG1

NM_004393.1

rs2131107

S14W

tcg/tgg

c

S

Probably damaging

IM

ENG

NM_000118.1

rs1800956

D366H

gac/cac

c

H

Possibly damaging

AN, DE, IM, MET

EPHX1

NM_000120.2

rs1051740

Y113H

tac/cac

c

H

Possibly damaging

IM, ME, PH

ERBB2

NM_004448.1

rs1058808

P1170A

ccc/gcc

g

A

Possibly damaging

IM, ST, TS/ON

F2R

NM_001992.2

rs2230849

Y187N

tac/aac

a

N

Probably damaging

IM

FPR1

NM_002029.3

rs867228

E346A

gag/gcg

c

A

Possibly damaging

IM

FUCA2

NM_032020.3

rs3762001

H371Y

cat/tat

t

Y

Possibly damaging

IM

GAA

NM_000152.2

rs1800307

G576S

ggc/agc

a

S

Possibly damaging

IM

GBP1

NM_002053.1

rs1048425

T349S

acc/agc

g

S

Possibly damaging

CS

GYS1

NM_002103.3

rs5453

P691A

cca/gca

g

A

Probably damaging

IM

GYS1

NM_002103.3

rs5456

K130E

aag/gag

g

E

Possibly damaging

IM

GYS1

NM_002103.3

rs5461

N283S

aat/agt

g

S

Possibly damaging

IM

HK2

NM_000189.4

rs2229629

R844K

agg/aag

g

R

Possibly damaging

IM, MIS

LIG4

NM_002312.2

rs1805388

T9I

act/att

t

I

Possibly damaging

DA, DD

MC1R

NM_002386.2

rs1805005

V60L

gtg/ttg

t

L

Possibly damaging

IM

MC1R

NM_002386.2

rs1805007

R151C

cgc/tgc

t

C

Probably damaging

IM

MC1R

NM_002386.2

rs3212366

F196L

ttc/ctc

c

L

Probably damaging

IM

MMP9

NM_004994.1

rs2250889

R574P

cgg/ccg

g

R

Possibly damaging

AN, IM

MMP9

NM_004994.1

rs3918252

N127K

aac/aag

g

K

Probably damaging

AN, IM

MNDA

NM_002432.1

rs2276403

H357Y

cac/tac

t

Y

Possibly damaging

GR, TR

MUC4

NM_004532.2

rs2259292

G88D

ggc/gac

g

G

Possibly damaging

IM

NFATC1

NM_006162.3

rs754093

C751G

tgt/ggt

g

G

Probably damaging

IM

NOTCH4

NM_004557.2

rs2071282

P203L

ccc/ctc

t

L

Probably damaging

IM, TS/ON

PGM3

NM_015599.1

rs473267

D466N

gat/aat

a

N

Possibly damaging

IM

PLAU

NM_002658.1

rs2227564

L141P

ctg/ccg

t

L

Possibly damaging

AN

PLAUR

NM_002659.1

rs4760

L317P

ctc/ccc

c

P

Possibly damaging

AN

PTGS2

NM_000963.1

rs5272

E488G

gag/ggg

g

G

Probably damaging

IM, MIS

PTPN3

NM_002829.2

rs3793524

A90P

gcc/ccc

g

A

Probably damaging

CC, CS

SLC1A5

NM_005628.1

rs3027956

P17A

ccc/gcc

g

A

Possibly damaging

IM

STAT2

NM_005419.2

rs2066816

Q66H

cag/cat

t

H

Possibly damaging

IM, ST

TBXAS1

NM_001061.2

rs5760

G390V

ggc/gtc

t

V

Probably damaging

IM

TBXAS1

NM_001061.2

rs5762

R425C

cgc/tgc

t

C

Probably damaging

IM

TBXAS1

NM_001061.2

rs5770

R261G

agg/ggg

g

G

Probably damaging

IM

TDG

NM_003211.2

rs4135113

G199S

ggc/agc

a

S

Possibly damaging

DD

TUBA1

NM_006000.1

rs3731891

R243C

cgc/tgc

t

C

Probably damaging

CS, MET

TYR

NM_000372.2

rs1042602

S192Y

tct/tat

a

Y

Possibly damaging

ME

VCAM1

NM_001078.2

rs3783613

G413A

ggt/gct

c

A

Possibly damaging

AN, CS, IM, MET

XRCC1

NM_006297.1

rs25489

R280H

cgt/cat

a

H

Possibly damaging

DD, DR, IM

XRCC1

NM_006297.1

rs1799782

R194W

cgg/tgg

t

W

Probably damaging

DD, DR, IM

  1. Abbreviations: AN = angiogenesis; BE = behaviour, CC = cell cycle; CS = cell signalling; DA = DNA adduct; DD = DNA damage; DE = development; GR = gene regulation; IM = immunology; ME = metabolism;
  2. MET = metastasis; MIS = miscellaneous; PH = pharmacology; ST = signal transduction; TS/ON = tumour suppressor/oncogene; TR = transcription.
  3. All nsSNPs are with ≥ 5 per cent minor allele frequency.
  4. a The gene symbols are as approved by the HUGO Gene Nomenclature Committee [67].
  5. b SNP identifiers (IDs) correspond to the dbSNP IDs (http://www.ncbi.nlm.nih.gov/SNP/) [31].
  6. c The position of the amino acid substitution and the amino acids specified by the major and minor SNP alleles are indicated.
  7. d The codons specified by the major and the minor SNP alleles are shown. The nucleotide change is underlined.
  8. e One-letter codes for the amino acids that are predicted to affect the protein function by PolyPhen.
  9. f The pathway(s) that the proteins are implicated in are as shown by the Cancer Genome Anatomy Project Genetic Annotation Initiative website (http://lpgws.nci.nih.gov/html-cgap/cgl/) [30].
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Human Genomics

ISSN: 1479-7364