Mutations in the KCNE1 gene encoding human minK which cause arrhythmia susceptibility thereby establishing KCNE1 as an LQT gene

Abstract

The genomic structure including the sequence of the intron/exon junctions is disclosed for KVLQT1 and KCNE1 which are genes associated with long QT syndrome. Additional sequence data for the two genes ARE also disclosed. Also disclosed are newly found mutations in KVLQT1 which result in long QT syndrome. The intron/exon junction sequence data allow for the design of primer pairs to amplify and sequence across all of the exons of the two genes. This can be used to screen persons for the presence of mutations which cause long QT syndrome. Assays can be performed to screen persons for the presence of mutations in either the DNA or proteins. The DNA and proteins may also be used in assays to screen for drugs which will be useful in treating or preventing the occurrence of long QT syndrome.

What is claimed is:  
     
         1 . A method for diagnosing the presence of a polymorphism in human KCNE1 (the coding region of which is bases 193-579 of SEQ ID NO:3) which causes long QT syndrome wherein said method is performed by means which identify the presence of said polymorphism, wherein said polymorphism is one which results in the presence of a KCNE1 polypeptide of SEQ ID NO:4 with an altered amino acid, said altered amino acid being selected from the group consisting of:: 
 a) an Asn at residue 76,    b) a Leu at residue 28,    c) a His at residue 32,    d) a Trp at residue 98,    e) an Ala at residue 127, and    f) a Thr at residue 127.    
     
     
         2 . The method of  claim 1 , wherein said polymorphism is selected from the group consisting of: 
 a) an A at base 418 of SEQ ID NO:3,    b) a T at base 275 of SEQ ID NO:3,    c) an A at base 287 of SEQ ID NO:3,    d) a T at base 484 of SEQ ID NO:3,    e) a G at base 571 of SEQ ID NO:3, and    f) an A at base 571 of SEQ ID NO:3.    
     
     
         3 . The method of  claim 1 , wherein said means comprises using a single-stranded conformation polymorphism technique to assay for said polymorphism.  
     
     
         4 . The method of  claim 1 , wherein said means comprises sequencing human KCNE1.  
     
     
         5 . The method of  claim 1 , wherein said means comprises performing an RNAse assay.  
     
     
         6 . The method of  claim 2 , wherein said means comprises using a single-stranded conformation polymorphism technique to assay for said polymorphism.  
     
     
         7 . The method of  claim 2 , wherein said means comprises sequencing human KCNE1.  
     
     
         8 . The method of  claim 2 , wherein said means comprises performing an RNAse assay.  
     
     
         9 . A method for diagnosing a polymorphism which causes long QT syndrome comprising determining the KCNE1 sequence in a patient by preparing cDNA from RNA taken from the patient and sequencing said cDNA to determine the presence or absence of a polymorphism selected from the group consisting of: 
 a) an A at base 418 of SEQ ID NO:3,    b) a T at base 275 of SEQ ID NO:3,    c) an A at base 287 of SEQ ID NO:3,    d) a T at base 484 of SEQ ID NO:3,    e) a G at base 571 of SEQ ID NO:3, and    f) an A at base 571 of SEQ ID NO:3.    
     
     
         10 . A method of assessing a risk in a human subject for long QT syndrome which comprises screening said subject for a polymorphism in a KCNE1 gene by comparing the sequence of the KCNE1 gene or its expression products isolated from a tissue sample of said subject with a wild-type KCNE1 gene or its expression products, wherein a polymorphism is selected from the group consisting of: 
 a) an A at base 418 of SEQ ID NO:3 or an Asn of residue 76 of SEQ ID NO:4,    b) a T at base 275 of SEQ ID NO:3 or a Leu of residue 28 of SEQ ID NO:4,    c) an A at base 287 of SEQ ID NO:3 or a His of residue 32 of SEQ ID NO:4,    d) a T at base 484 of SEQ ID NO:3 or a Trp of residue 98 of SEQ ID NO:4,    e) a G at base 571 of SEQ ID NO:3 or a Ala of residue 127 of SEQ ID NO:4, and    f) an A at base 571 of SEQ ID NO:3 or a Thr of residue 127 of SEQ ID NO:4.    
     
     
         11 . The method of  claim 10 , wherein said expression product is selected from the group consisting of mRNA of the KCNE1 gene (SEQ ID NO:3) and a KCNE1 polypeptide (SEQ ID NO:4) encoded by the KCNE1 gene.  
     
     
         12 . The method of  claim 10 , wherein one or more of the following procedures is carried out: 
 (a) observing shifts in electrophoretic mobility of single-stranded DNA from said sample on non-denaturing polyacrylamide gels;    (b) hybridizing a KCNE1 gene probe to genomic DNA isolated from said sample under conditions suitable for hybridization of said probe to said gene;    (c) determining hybridization of an allele-specific probe to genomic DNA from said sample;    (d) amplifying all or part of the KCNE1 gene from said sample to produce an amplified sequence and sequencing the amplified sequence;    (e) determining by nucleic acid amplification the presence of a specific KCNE1 polymorpic allele in said sample;    (f) molecularly cloning all or part of the KCNE1 gene from said sample to produce a cloned sequence and sequencing the cloned sequence;    (g) determining whether there is a mismatch between molecules (1) KCNE1 gene genomic DNA or KCNE1 mRNA isolated from said sample, and (2) a nucleic acid probe complementary to the human wild-type KCNE1 gene DNA, when molecules (1) and (2) are hybridized to each other to form a duplex;    (h) amplification of KCNE1 gene sequences in said sample and hybridization of the amplified sequences to nucleic acid probes which comprise wild-type KCNE1 gene sequences;    (i) amplification of KCNE1 gene sequences in said tissue and hybridization of the amplified sequences to nucleic acid probes which comprise mutant KCNE1 gene sequences;    (j) screening for a point mutation;    (k) determining in situ hybridization of the KCNE1 gene in said sample with one or more nucleic acid probes which comprise the KCNE1 gene sequence or a polymorphic KCNE1 gene sequence;    (l) immunoblotting;    (m) immunocytochemistry;    (n) assaying for binding interactions between KCNE1 gene protein isolated from said tissue and a binding partner capable of specifically binding the polypeptide expression product of a KCNE1 polymorphic allele and/or a binding partner for the KCNE1 polypeptide having the amino acid sequence set forth in SEQ ID NO:4; and    (o) assaying for the inhibition of biochemical activity of said binding partner.