Nktcn1 QTL Detail

Summary

• Symbol
  Nktcn1
• Name
  natural killer T cell numbers 1
• Synonyms
  Nkt1

• Feature Type
  QTL
• IDs
  MGI:2681136
  NCBI Gene: 493025
• Candidate Genes
  2 Genes

Location &
Maps

• Sequence Map
  Chr1:168186243-171632257 bp

  From MGI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 1, 76.25 cM (cM position of peak correlated region/marker)
• Mapping Data
  3 experiments

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  2 phenotypes from 2 alleles in 2 genetic backgrounds
  4 phenotype references
  

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

Sequences &
Gene Models

• NCBI Gene
  493025

References

• Summaries
  All 7

  Phenotypes 4
• Earliest
  J:85376 Esteban LM, et al., Genetic control of NKT cell numbers maps to major diabetes and lupus Loci. J Immunol. 2003 Sep 15;171(6):2873-8
• Latest
  J:170693 Jordan MA, et al., Role of SLAM in NKT Cell Development Revealed by Transgenic Complementation in NOD Mice. J Immunol. 2011 Apr 1;186(7):3953-65

Candidate Genes for Nktcn1:

Gene	Genome Location (GRCm39)	Reference	QTL Note
Slamf1	Chr1:171594700-171628752 (+)	J:137521	Microarray analysis was performed on thymus RNA from 4 week old NOD.Nkrp1.Nkt1 congenic animals and NOD.Nkrp1 congenic animals to screen candidate genes for Nktcn1. The NOD.Nkrp1 congenic carries C57BL/6J-derived DNA from D6Mit105 (45.5 cM) toD6Mit135 (62.3 cM) on a NOD genetic background. The NOD.Nkrp.Nkt1 congenic carries C57BL/6J-derived DNA from D1Mit369 (73 cM) to D1Mit155 (telomere) on a NOD genetic background in addition to the NOD-derived chromosome 6 interval. The formal QTL designation for Nkt1 is Nktcn1. Nkrp1 is synonymous with Klrb1c. Previously identified lupus susceptibility locus Sle1b (89.5 cM) maps near Nktcn1. Twenty-one genes displaying expression differences between NOD and C57BL/6J mapped to the Nktcn1 region, 15of which are located in the 95% confidence interval. The most promising candidate genes for controlling NKT cell number are Slamf1 (93.3 cM) and Slamf6 (89.5 cM). Gene expression of Slamf1 and Slamf6 was examined in thymic and splenic lymphocytes from congenic animals. It was observed that NOD.Nkrp.Nkt1 animals expressed significantly higher amounts of SLAM proteins on cell sufaces compared to NOD.Nkt1 parentals. Authors hypothesize control of NKT cell numbers may be mediated by differentialexpression of Slamf1 with additionial influence by Slamf6.
Slamf6	Chr1:171745002-171776525 (+)	J:137521	Microarray analysis was performed on thymus RNA from 4 week old NOD.Nkrp1.Nkt1 congenic animals and NOD.Nkrp1 congenic animals to screen candidate genes for Nktcn1. The NOD.Nkrp1 congenic carries C57BL/6J-derived DNA from D6Mit105 (45.5 cM) toD6Mit135 (62.3 cM) on a NOD genetic background. The NOD.Nkrp.Nkt1 congenic carries C57BL/6J-derived DNA from D1Mit369 (73 cM) to D1Mit155 (telomere) on a NOD genetic background in addition to the NOD-derived chromosome 6 interval. The formal QTL designation for Nkt1 is Nktcn1. Nkrp1 is synonymous with Klrb1c. Previously identified lupus susceptibility locus Sle1b (89.5 cM) maps near Nktcn1. Twenty-one genes displaying expression differences between NOD and C57BL/6J mapped to the Nktcn1 region, 15of which are located in the 95% confidence interval. The most promising candidate genes for controlling NKT cell number are Slamf1 (93.3 cM) and Slamf6 (89.5 cM). Gene expression of Slamf1 and Slamf6 was examined in thymic and splenic lymphocytes from congenic animals. It was observed that NOD.Nkrp.Nkt1 animals expressed significantly higher amounts of SLAM proteins on cell sufaces compared to NOD.Nkt1 parentals. Authors hypothesize control of NKT cell numbers may be mediated by differentialexpression of Slamf1 with additionial influence by Slamf6.