Table 2 Filtered variants from whole-genome analysis. Variants with predicted high or moderate effects and a homozygous mutant genotype exclusively found in the LS-affected pool as well as a heterozygous or homozygous wild-type genotype in the LS-unaffected pool are shown. All five reference dogs of four different breeds do not show the mutant genotype. Potential functional effects of these variants were predicted using SIFT and PolyPhen

1

13398018

T>G

T>P/ S>R

missense variant

1/1

0/0

0/0

ENSCAFG00000031329 (novel gene; (ENSCAFT00000043665) and ENSCAFG00000030129 (novel gene; ENSCAFT00000048679)

tolerated (0.07)/ deleterious (0.02)

benign (0.074)/-

1

111903572

A>G

T>A

missense variant

1/1

0/1

0/0

CEACAM1 (ENSCAFT00000007749/ ENSCAFT00000046087/ ENSCAFT00000022623/ ENSCAFT00000047331/ ENSCAFT00000049292)

tolerated (0.08/ 0.13/ 0.2/ 0.21/ 0.2)

benign (0.00)/ benign (0.310)/ possibly damaging (0.659)/ possibly damaging (0.605)/ benign (0.250)

3

56483857

G>T

P>T

missense variant

1/1

0/1

0/0

IL16 (ENSCAFT00000021964)

tolerated (0.59)

benign (0.310)

3

62265062

A>T

F>I

missense variant

1/1

0/1

0/0

ENSCAFG00000017475 (novel gene; ENSCAFT00000027691)

deleterious (0.01)

possibly damaging (0.614)

5

16233038

G>T

L>M

missense variant

1/1

0/1

0/0

CEP164 (ENSCAFT00000020686)

deleterious (0.02)

probably damaging (0.996)

6

67204999

C>T

R>Q

non coding transcript variant

1/1

0/1

0/0

ENSCAFG00000005648 (novel gene; ENSCAFT00000009086)

-

-

6

67205308

A>C

Y>* (stop codon)

non coding transcript variant

1/1

0/1

0/0

ENSCAFG00000005648 (novel gene; ENSCAFT00000009086)

-

-

6

67205754

G>A

R>* (stop codon)

non coding transcript variant

1/1

0/1

0/0

ENSCAFG00000005648 (novel gene; ENSCAFT00000009086)

-

-

6

67205959

A>G

L>P

non coding transcript variant

1/1

0/1

0/0

ENSCAFG00000005648 (novel gene; ENSCAFT00000009086)

-

-

6

67205966

T>G

T>P

non coding transcript variant

1/1

0/1

0/0

ENSCAFG00000005648 (novel gene; ENSCAFT00000009086)

-

-

7

2590167

G>A

S>N

missense variant

1/1

0/1

0/0

KIF14 (ENSCAFT00000017720)

tolerated (0.21)

benign (0.002)

7

4169250

A>T

F>Y

missense variant

1/1

0/1

0/0

PTPRC (ENSCAFT00000017964/ ENSCAFT00000017955)

tolerated (0.3/ 0.31)

benign (0.023/

0.347 )

8

22616300

C>T

P>L

missense variant

1/1

0/1

0/0

FANCM (ENSCAFT00000046644/ ENSCAFT00000022327/ ENSCAFT00000048988)

tolerated (0.42/ 0.34/ 0.42)

benign (0.009/ 0.009/ 0.004 )

8

47544408

G>A

G>R

missense variant

1/1

0/1

0/0

VRTN (ENSCAFT00000026784)

tolerated (0.56)

possibly damaging (0.560)

8

73685892

C>G

Q>H

missense variant

1/1

0/1

0/0

ENSCAFG00000029996 (novel gene; ENSCAFT00000049952)

deleterious (0)

benign (0.152)

8

73685923

C>G

W>S

missense variant

1/1

0/1

0/0

ENSCAFG00000029996 (novel gene; ENSCAFT00000049952)

deleterious (0)

probably damaging (1.000)

8

73685927

T>G

S>R

missense variant

1/1

0/1

0/0

ENSCAFG00000029996 (novel gene; ENSCAFT00000049952)

tolerated (0.21)

probably damaging (0.963)

9

37739213

C>T

R>W

missense variant

1/1

0/1

0/0

ENSCAFG00000032731 (novel gene; ENSCAFT00000047013)

tolerated (0.07)

probably damaging (0.998)

9

51227945

T>C

H>R

missense variant

1/1

0/1

0/0

ENSCAFG00000019863 (novel gene; ENSCAFT00000031603)

deleterious (0)

possibly damaging (0.898)

10

36330685

C>T

A>V

missense variant

1/1

0/1

0/0

FAM32A (ENSCAFT00000003279)

tolerated (0.16)

benign (0.328)

11

67454670

A>C

S>R

missense variant

1/1

0/1

0/0

ENSCAFG00000028946

(novel gene; ENSCAFT00000045538)

tolerated (0.33)

-

12

40430108-40430109

A>AGG

R47fs

frameshift variant

1/1

0/1

0/0

ENSCAFG00000030790 (novel gene; ENSCAFT00000045206)

-

-

12

52354031

A>G

F>S

missense variant

1/1

0/1

0/0

ENSCAFG00000030881 (novel gene;

ENSCAFT00000046435)

deleterious (0.01)

-

12

52354041

G>A

L>F

missense variant

1/1

0/1

0/0

ENSCAFG00000030881 (novel gene;

ENSCAFT00000046435)

deleterious (0.02)

-

14

16187782

T>G

I>M

missense variant

1/1

0/1

0/0

CFAP69 (ENSCAFT00000002973)

tolerated (0.23)

possibly damaging (0.648)

14

22993351

A>T

C>S

missense variant

1/1

0/1

0/0

COL28A1 (ENSCAFT00000044570)

deleterious (0)

probably damaging (1.000)

18

39577830

C>T

A>V

missense variant

1/1

0/1

0/0

ENSCAFG00000030998 (novel gene; ENSCAFT00000047197)

tolerated (1)

benign (0.000)

20

54722514

rs22884799

T>C

I>M

missense variant

1/1

0/1

0/0

KDM4B (ENSCAFT00000030040)

tolerated (0.7)

possibly damaging (0.728)

27

2322565

C>T

R>C

missense variant

1/1

0/1

0/0

KRT3 (ENSCAFT00000011634)

deleterious (0.03)

possibly damaging (0.942)

28

31706107

A>C

N>T

missense variant

1/1

0/1

0/0

ENSCAFG00000012412 (novel gene; (ENSCAFT00000019700)

tolerated (0.78)

benign (0.000)

32

21555092

C>T

D>N

missense variant

1/1

0/1

0/0

TRMT10A (ENSCAFT00000016732)

tolerated (0.31)

probably damaging (0.997)

34

22046092

C>G

E>Q

missense variant

1/1

0/1

0/0

LEPREL1 (ENSCAFT00000022188)

tolerated (0.43)

possibly damaging (0.945)

X

96702059

rs24643372

A>G

R>G

missense variant

1/1

0/1

0/0

ENSCAFG00000029138 (novel gene; ENSCAFT00000044717)

tolerated (0.41)

benign (0.001)