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Table 4 Significant breed-specific P-values for nonsynonmous variants

From: Whole genome sequencing for the investigation of canine mammary tumor inheritance - an initial assessment of high-risk breast cancer genes reveal BRCA2 and STK11 variants potentially associated with risk in purebred dogs

Gene

RS ID Number

Variant Name

Protein Name

Variant Type

Polyphen Score

MAF in EVA Control Cohort (%)

CMT Cohort

Total Cohort

Breed Specific

Dalmatian

Golden Retriever

Siberian Husky

Standard Schnauzer

MAF (%)

P-value

MAF (%)

P-value

MAF (%)

P-value

MAF (%)

P-value

MAF (%)

P-value

BRCA2: ENSCAFT00000010309.3

rs23250374

c.A428G

p.H143R

missense

BENIGN

25.7

42.9

0.0749

33.3

0.6506

70

0.0048

0

0.3447

50

0.1847

rs850935038**

c.T1158G**

p.C386W**

missense

BENIGN

20.6

42.9

0.0095

50

0.1107

10

0.6948

83.3

0.0096

50

0.1107

rs853007536**

c.9995_9996insAAA**

p.M3332delinsIK**

indel

NA

20.9

42.9

0.01621

50

0.1136

10

0.695

83.3

0.0006

50

0.1136

STK11: ENSCAFT00000031055.3

–

c.C109T^

p.P37S^

missense

UNKNOWN

0

3.6

0.0654

16.7

0.0148

0

1

0

1

0

1

–

c.A286G^

p.M96V^

missense

BENIGN

0

10.7

0.0003

0

1

0

1

33.3

0.0002

16.7

0.0148

–

c.T293C^

p.F98S^

missense

BENIGN

0

10.7

0.0003

0

1

0

1

33.3

0.0002

16.7

0.0148

  1. ** Major allele corresponds to the alternate allele, not the reference allele (based on EVA control data)
  2. ^ P-values for these variants were generated following the assumption that 200 of the control dogs were successfully sequenced in this location, and no mutations were identified