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Table 2 Results from filtering analysis for SPAID-associated genotypes

From: Whole genome sequencing identifies missense mutation in MTBP in Shar-Pei affected with Autoinflammatory Disease (SPAID)

CFA

Position

Base change

Amino acid change

Consequence

Genotype (5 reference dogs)

Genotype (2 affected Shar-Pei)

Gene (transcript)

SIFT

PolyPhen-2

1

8186638

A > G

K > R

missense variant

0/0

1/1

RTTN (ENSCAFT00000000055)

tolerated (0.3)

benign (0.036)

1

112413056

T > C

K > E/K > E

missense variant

0/0

1/1

CD79A (ENSCAFT00000037106/ENSCAFT00000008000)

tolerated low confidence

benign (0.227)

1

112413114

C > CGTGATG

I67_T68dup/I67_T68dup

disruptive inframe insertion

0/0

1/1

CD79A (ENSCAFT00000037106/ENSCAFT00000008000)

NA

NA

3

14027517

A > C

L > R

missense variant

0/0

1/1

ARSK (ENSCAFT00000012646)

deleterious low confidence

probably damaging (0.993)

4

6374801

G > A

C > Y

missense variant

0/0

1/1

PCNXL2 (ENSCAFT00000018397)

deleterious low confidence

NA

4

19114717

GT

D > E/D > E

missense variant

0/0

1/1

DNAJC12 (ENSCAFT00000021116/ENSCAFT00000049485)

tolerated (0.1/0.28)

benign/possibly damaging (0.023/0.579)

4

75351270

A > G

V > A

missense variant

0/0

1/1

PDZD2 (ENSCAFT00000047348)

tolerated (0.33)

benign (0.000)

5

21123033

C > T

R > Q/R > Q/R > Q

missense variant

0/0

1/1

DIXDC1 (ENSCAFT00000022334/ENSCAFT00000022333/ENSCAFT00000035298)

tolerated (1/1/1)

benign (0.000/0.003/0.001)

5

48648175

G > C

-

non coding transcript exon variant, non coding transcript variant

0/0

1/1

ENSCAFG00000018860 (novel gene; ENSCAFT00000029943)

NA

NA

5

60223074

G > T

P > Q

missense variant

0/0

1/1

ACOT7 (ENSCAFT00000049704)

deleterious low confidence

possibly damaging (0.694)

6

36821482

G > T

S > Y

missense variant

0/0

1/1

C16orf96 (ENSCAFT00000048346)

deleterious (0)

probably damaging (0.995)

6

38937765

C > T

A > V

missense variant

0/0

1/1

ZNF598 (ENSCAFT00000030940)

tolerated (0.62)

benign (0.017)

6

40648375

C > T

P > S/P > S/P > S

missense variant

0/0

1/1

ENSCAFG00000024344 (novel gene; ENSCAFT00000037586/ENSCAFT00000037216/ENSCAFT00000037580)

deleterious (0/0/0)

probably damaging (1.00/1.00/1.00)

6

56637047

TACAA > T

F76fs

frameshift variant

0/0

1/1

RPAP2 (novel gene; ENSCAFT00000032095)

NA

NA

6

56760354

T > C

K > E

missense variant

0/0

1/1

KIAA1107 (ENSCAFT00000032101)

tolerated (0.26)

benign (0.053)

6

56786359

G > C

D > E

missense variant

0/0

1/1

KIAA1107 (ENSCAFT00000032101)

tolerated (1)

benign (0.000)

6

57204844

A > G

Y > C

missense variant

0/0

1/1

TGFBR3 (ENSCAFT00000032134)

deleterious (0)

probably damaging (0.998)

9

3074837

G > C

H > Q/H > Q/H > Q

missense variant

0/0

1/1

TNRC6C (ENSCAFT00000048770/ENSCAFT00000050041/ENSCAFT00000008443)

tolerated (0.12/0.8/0.72)

probably damaging (0.999/0.988/0.999)

11

62457942

G > A

A > T

missense variant

0/0

1/1

ZNF462 (ENSCAFT00000004432)

NA

benign (0.000)

13

19383758

G > A

E > K

missense variant

0/0

1/1

MTBP (ENSCAFT00000001477)

deleterious (0.01)

probably damaging (0.979)

13

58949521

C > G

L > V/L > V

missense variant

0/0

1/1

UGT2B31 (ENSCAFT00000022724/ENSCAFT00000004520)

tolerated (1/1)

benign (0.000/0.000)

13

58949524

G > A

V > I/V > I

missense variant

0/0

1/1

UGT2B31 (ENSCAFT00000022724/ENSCAFT00000004520)

tolerated (0.49/0.48)

benign (0.005/0.001)

13

58949536

A > G

T > A/T > A

missense variant

0/0

1/1

UGT2B31 (ENSCAFT00000022724/ENSCAFT00000004520)

tolerated (0.66/0.65)

benign (0.000/0.000)

15

42583230

A > C

N > H/N > H

missense variant

0/0

1/1

HCFC2 (ENSCAFT00000011975/ENSCAFT00000011972)

tolerated (0.09)/deleterious (0.04)

possibly damaging (0.583/0.616

17

58777715

G > A

S > L

missense variant

0/0

1/1

TXNIP (ENSCAFT00000018124)

tolerated (0.2)

benign (0.126)

18

40794747

C > T

R > H

missense variant

0/0

1/1

OR10H12 (ENSCAFT00000037956)

tolerated (0.37)

benign (0.000)

20

54717650

G > A

T > M

missense variant

0/0

1/1

KDM4B (ENSCAFT00000030040)

tolerated (0.05)

possibly damaging (0.934)

20

54729635

A > G

-

splice acceptor variant

0/0

1/1

KDM4B (ENSCAFT00000030040)

NA

NA

22

30574626

C > T

T > M

missense variant

0/0

1/1

CLN5 (ENSCAFT00000008156)

deleterious (0.01)

probably damaging (1.000)

24

46507770

C > T

R > W

missense variant

0/0

1/1

ENSCAFG00000030917 (novel gene; ENSCAFT00000046966)

NA

NA

27

31792218

T > C

I > V

missense variant

0/0

1/1

C12orf60 (ENSCAFT00000020587)

tolerated (0.39)

benign (0.009)

28

34998871

G > A

V > I

missense variant

0/0

1/1

BCCIP (ENSCAFT00000020430)

tolerated (0.24)

possibly damaging (0.992)

30

29440908

C > T

E > K

missense variant

0/0

1/1

RASL12 (ENSCAFT00000027120)

tolerated (0.08)

benign (0.034)

30

29986720

G > A

E > K

missense variant

0/0

1/1

SLC24A1 (ENSCAFT00000027314)

tolerated (0.09)

benign (0.223)

32

22124585

GTCTTT > G

K64fs

frameshift variant (microsatellite)

0/0

1/1

ENSCAFG00000031054 (novel gene; ENSCAFT00000047190)

NA

NA

37

502225

CCTTGTGCAA > C

L4_K6del

inframe deletion

0/0

1/1

OSGEPL1 (ENSCAFT00000014928)

NA

NA

38

20346455

T > A

V > D

missense variant

0/0

1/1

C1orf111 (ENSCAFT00000036623)

tolerated (0.94)

benign (0.000)

  1. In total 37 variants with predicted high or moderate effects (SNPEff) could be exclusively found homozygous for the mutant allele in SPAID-affected Shar-Pei. SIFT and PolyPhen-2 variant effect estimations are shown for each position