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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