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Table 5 Exclusion of potential linkage within 10 Mb of Isl1 (117098488) and on the remainder of chromosome 13

From: Exome sequencing identifies a missense mutation in Isl1associated with low penetrance otitis media in dearisch mice

Gene name Position Reference Dearisch Type Location Zygosity Consequence (if in coding region)a
Within 10 Mb of Isl1        
   Ipo11 107700899 * -T/* Deletion Splice site (intronic) Het  
   Kif2a 107752127 * */-G Deletion 3' UTR Het  
   Slc38a9 113523874 * -TT/-TT Deletion 5' UTR Hom  
   Gzmk 113963370 * */+T Insertion Splice site Het  
On remainder of chromosome 13        
   Pfkp 6604227 * */+GG Insertion Exonic Het Frameshift leading to truncation of protein in exon 10 (approximately half its length)
   Gtpbp4 8984980 * */-A Deletion Splice site (intronic) Het  
   Pgbd1 21515496 * -AGGAA/-AGGAA Deletion Splice site (intronic) Hom  
   Isca1 21587150 * */-GGCTGCGG Deletion 5' UTR Het  
   Hist1h1c 23831772 * +TN/+TN Insertion 3' UTR Hom  
   Hist1h1a 23856249 A A/C SNP 3' UTR Het  
   Agtr1a 30473986 * */-T Deletion 3' UTR Het  
   Txndc5 38599758 * */-A Deletion Splice site (intronic) Het  
   Gm9979 40801514 * +CACACACACACG/* Insertion 3' UTR Het  
   Tpmt 47135375 A A/T SNP Noncoding (retained intron) Het  
   Iars 49829191 * */-TG Deletion 3' UTR Het  
   Sema4d 51798481 * */+G Insertion Exonic Het Frameshift leading to truncation of protein in last exon
   Cdhr2 54827830 * */+G Insertion Exonic Het Frameshift leading to truncation of protein in exon 19 (approximately two-thirds of its length)
   Smad5 56824847 * */+CACACACACACA Insertion 5' UTR Het  
   Smad5 56824796 C C/T SNP 5' UTR Het  
   Klhl3 58165232 * -GA/-GA Deletion Splice site (intronic) Hom  
   Ptch1 63613020 * */+A Insertion Exonic Het Frameshift leading to truncation of protein very close to carboxyl terminus
   1110018J18Rik 64393367 * +A/* Insertion 3' UTR Het  
   Sdha 74460494 T G/T SNP 3' UTR Het  
   Spata9 76115351 * -C/-C Deletion Exonic Hom Frameshift leading to incorrect final 15 amino acids and loss of stop codon
   Fam81b 76408769 * +TTA/+TTA Insertion Exonic Hom Gain of stop codon leading to truncation of protein after 15 amino acids
   Rasa1 85370111 * +G/+G Insertion Noncoding (retained intron) Hom  
   Rasgrf2 92024132 * -A/-A Deletion Splice site (intronic) Hom  
   Pde8b 95822955 * */-TAA Deletion Noncoding (retained intron) Het  
   Bdp1 100808235 * */+A Insertion Splice site (intronic) Het  
  1. aPredicted consequences are shown where the mutation lies in a coding region. Plus signs indicate insertion; minus signs indicate deletion. *Asterisks indicate the presence of the wildtype reference sequence where an insertion or deletion has been called in the dearisch sequence. These calls have not been confirmed by capillary sequencing.