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Table 2 PTPN22 sequence variants identified by sequencing genomic DNA from three atopic and three non-atopic WHWTs.

From: PTPN22 polymorphisms may indicate a role for this gene in atopic dermatitis in West Highland white terriers

Sequence variant identity

Position on CFA17 (bp)a,b

Predicted location in gene

Nucleotide in reference databaseb

Sequence of variant

Reference SNP identity

Predicted functional effectc

Variant risk score c

Atopic dogs

Non-atopic dogs

Cross-species conservation of variant nucleotide sequenceb,d

        

Dog 1

Dog 2

Dog 3

Dog 4

Dog 5

Dog 6

 

1

54759173

UTR

C

T

rs22597162

Transcription regulatory (score 86.5)

1-3

C/C

C/T

C/T

C/C

C/C

C/C

Conserved in 10/10

2

54759006

UTR

A

del

New variant (dbSNP ss 315790492)

Transcription regulatory (score 87.7)

1-3

del/del

del/A

del/A

T/A

del/A

A/A

Conserved in 9/10

3

54742593

Intronic

A

G

rs22597162

NA

0-2

G/G

G/A

G/A

G/G

G/G

G/G

Not conserved

4

54742027

Intronic

A

T

rs22559551

NA

0-2

T/T

T/A

T/A

A/A

T/A

A/A

Conserved in 6/10

5

54739568

Intronic

T

C

rs22559538

NA

No risk

T/T

C/T

C/T

C/C

C/T

C/C

Not conserved

6

54739315

Intronic

A

G

New variant (dbSNP ss 315790493)

NA

0-2

G/G

G/G

G/G

A/A

A/G

A/A

Not conserved

7

54738923

Intronic

G

del

New variant (dbSNP ss 15790494)

NA

No risk

del/del

del/del

del/del

del/del

del/del

del/del

NA

8

54738927

Intronic

-

A

New variant (dbSNP ss 315790495)

NA

No risk

A/A

A/A

A/A

A/A

A/A

A/A

NA

9

54734456

Intronic

T

C

rs22559532

NA

0-2

C/C

C/T

C/T

C/C

C/C

C/C

Not conserved

10

54734415

Intronic

A

G

rs22559522

NA

No risk

A/A

A/G

A/G

G/G

A/G

G/G

Conserved in 10/10

11

54717953

Exonic

G

A

New variant (dbSNP ss 315790496)

Synonymous Splicing regulatory (score 85.4)

1-4

G/G

G/G

G/G

A/A

A/A

A/A

Conserved in 7/10

12

54715779

Intronic

T

C

rs22578128

NA

0-2

C/C

C/T

C/T

T/T

C/T

T/T

Conserved in 2/10

13

54709793

Intronic (spice site)

17-T repeat (wild)

22-T repeat (variant)

New variant (dbSNP ss 315790497)

Alternative splicing regulatory (score 3.39)

3-4

variant/variant

variant/wild

variant/wild

wild/wild

variant/wild

wild/wild

Conserved in 10/10

14

54699432

UTR

C

T

New variant (dbSNP ss 315790498)

NA

0-2

C/C

C/C

C/C

T/T

T/T

T/T

Not conserved

15

54698793

UTR

G

T

New variant (dbSNP ss 315790499)

NA

1-3

T/T

T/T

T/T

T/T

T/T

T/T

NA

16

54698788

UTR

C

T

New variant (dbSNP ss 315790500)

Transcription regulatory (score 85.4)

1-3

T/T

T/T

T/T

C/C

C/C

C/C

Conserved in 7/10

17

54698729

UTR

T

C

New variant (dbSNP ss 315790501)

NA

1-3

C/C

C/C

C/C

C/C

C/C

C/C

NA

18

54698473

UTR

G

T

New variant (dbSNP ss 315790502)

NA

0

T/T

T/T

T/T

G/G

G/T

G/G

Conserved in 9/10

  1. Sequence variants with a predicted medium to high disease-associated functional effect, with strongly conserved sequence across 10 mammals (dog, human, pig, horse, mouse, rat, cattle, chimpanzee, gorilla and orangutan) and differential distribution between atopic and non-atopic dogs are underlined (Sequence variant identities 1, 2, 11, 13 and 16)
  2. areverse strand; bbased on the 1.5× poodle genome (version 1) and the boxer 7.6× whole-genome sequences (CanFam2.0), accessed in March 2010 from http://www.ncbi.nlm.nih.gov and http://genome.ucsc.edu; cas predicted by FASTSNP [5]; disease-risk possibilities are 0 (no potential functional risk), 1 (very low risk), 2 (low risk), 3 (medium), 4 (high risk) and 5 (very high risk); FASTSNP provides a "risk score" for each SNP based on its putative biological function; danalyzed following genomic alignment of flanking regions containing the genetic variants in 10 possible species (dog, human, pig, horse, mouse, rat, cattle, chimpanzee, gorilla and orangutan); UTR: untranslated region (DNA); NA: not accessed; del: nucleotide deletion
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BMC Research Notes

ISSN: 1756-0500

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