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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.