Cq4 QTL Detail

Summary

• Symbol
  Cq4
• Name
  cholesterol QTL 4

• Feature Type
  QTL
• IDs
  MGI:3624134
  NCBI Gene: 100035302
• Candidate Genes
  1 Gene

Location &
Maps

• Sequence Map
  Chr9:32411751-32411890 bp

  From MGI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 9, 17.80 cM (cM position of peak correlated region/marker)
• Mapping Data
  2 experiments

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  1 phenotype from 2 alleles in 1 genetic background
  1 phenotype reference
  

• All Mutations and Alleles
  2
• QTL
  2
• Find Mice (IMSR)
  0 strains or lines available

Sequences &
Gene Models

• NCBI Gene
  100035302

References

• Summaries
  All 3

  Phenotypes 1
• Earliest
  J:87328 Suto J, et al., Quantitative trait locus analysis of plasma cholesterol and triglyceride levels in KK x RR F2 mice. Biochem Genet. 2003 Oct;41(9-10):325-41
• Latest
  J:99474 Suto J, Apolipoprotein gene polymorphisms as cause of cholesterol QTLs in mice. J Vet Med Sci. 2005 Jun;67(6):583-9

Candidate Genes for Cq4:

Gene	Genome Location (GRCm39)	Reference	QTL Note
Apoa4	Chr9:46152142-46154756 (+)	J:99474	Linkage analysis was performed on 3 separate F2 crosses in 3 previous studies: J: 54322, J:87328 and J:94251 to map QTLs associated with plasma cholesterol levels. Cq1, Cq2, and Cq6 mapped to mouse Chromosome 1, Cq3 mapped to mouse Chromosome 3, and Cq4 and Cq5 mapped to mouse Chromosome 9. Cq2 and Cq6 map to the same location on distal mouse Chromosome 1 at approximately 100 cM. Cq2 was identified in a (C57BL/6J x KK-A)F2 intercross and Cq6 was identified in a (C57BL/6J x RR)F2 intercross. Apoa2 wasinvestigated as a possible candidate gene. The Apoa2 allele is found in KK and RR strains and is associated with increased cholesterol levels while inbred strain C57BL/6J carries the Apoa2 allele. It is thought that the Apoa2 allele may be responsible for the QTL effects of Cq2 and Cq6. Inbred strains A/J and SM/J carry the Apoa2 allele. It was previously unknown whether the Apoa2 and Apoa2 alleles had the same or different influences on plasma cholesterol level. An F2 intercross between congenic strains C57BL/6J-Apoa2 and C57BL/6J-Apoa2 revealed no physiological differences between the Apoa2 and Apoa2 alleles. Therefore, the Apoa2 allele confers increased plasma cholesterol compared to the Apoa2 and Apoa2 alleles. Cq4 and Cq5 map to the same location on mouse Chromosome 9 at approximately 27 cM and Apoa1 and Apoa4 were investigated as possible candidate genes. Cq4 was identified in a (C57BL/6J x KK-A)F2 intercross and Cq5 was identified in a (KK x RR)F2 intercross. Sequence analysis of Apoa1 revealed that polymorphic differences between the involved strains did not correlate to cholesterol phenotype. Analysis of Apoa4 revealed a silent polymorphism (C771T) that exhibits complete correlation to cholesterol phenotype. Inbred strain KK carries the T allele whereas inbred strain C57BL/6J and RR carry the C allele. Another polymorphism in Apoa4 was detected involving a 12 nucleotide insertion encoding Glu-Gln-Ala/Val-Gln. Inbred strain KK carries 3 repeats, inbred strain C57BL/6J carries 4 repeats, and inbred strain RR carries 5 repeats. However, it could not be determined if this particular polymorphism explains the QTL effect of Cq4 and Cq5 on cholesterol levels.