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QTL Variant Detail
QTL variant: Smcl1CBA/J
Name: smoke-mediated chord length 1; CBA/J
MGI ID: MGI:6317230
QTL: Smcl1  Location: Chr16:54015309-58330871 bp  Genetic Position: Chr16, Syntenic
Strain of Specimen:  CBA/J
Allele Type:    QTL
Inheritance:    Not Specified

Mapping and Phenotype information for this QTL, its variants and associated markers


Chronic obstructive pulmonary disease (COPD) is caused by a complex interaction of environmental exposures, most commonly cigarette smoke, and genetic factors. Chronic cigarette smoke exposure in the mouseis a commonly used animal model of COPD.

The authors aimed to expand knowledge about the variable susceptibility of inbred strains to this model and test for genetic variants associated with this trait. Alveolar chord length (CL) was measured after 6 months of exposure to cigarette smoke or room air in 34 inbred strains of mice (129S1/SvImJ, A/J, AKR/J, BALB/cByJ, BALB/cJ, BPN/3J, BTBRT1tf/J, BUB/BnJ, C3H/HeJ,C57BL/10J, C57BL/6J, C57BLKS/J, C57BR/cdJ, C57L/J, CBA/J, CE/J, DBA/1J, DBA/2J, FVB/NJ, I/LnJ, KK/HlJ, LG/J, LP/J, MRL/MpJ, NOD/ShiLtJ, NON/ShiLtJ, NZO/HlLtJ, NZW/LacJ, P/J, PL/J, RIIIS/J, SJL/J, SM/J, and SWR/J).

A/J was the most susceptible strain in the survey (delta CL 7.0 +/- 2.2 micrometers) and CBA/J was the least susceptible (delta CL 20.3 +/- 1.2 micrometers).

The authors tested for association of smoke-mediated chord length (SMCL) with known genotypes of the 34 inbred strains. Testing for association between SMCL and 4 million SNPs published by the National Institute of Environmental Health Sciences was performed using the genome-wide efficient mixed model algorithm (GEMMA), which partially corrects for the complex population structure of the inbred strains in this survey. All SNPs were aligned to NCBI B37.

The most significant association the authors identified was with rs46114044 located at Chr16: 54194946 (P = 7.21 x 10^-5).

This locus has been named Smcl1 (smoke-mediated chord length 1).

To account for the significant linkage disequilibrium in the mouse, the authors defined a 4.3 Mb region surrounding this association at Chr16: 54194946 - 58510508 as the candidate region to integrate with human GWAS results.

By integrating mouse and human genome-wide scans, the authors identified the candidate gene Abi3bp. CBA/J mice harbor predicted deleterious variants in Abi3bp, and expression of the gene differs significantly between CBA/J and A/J mice.

Original:  J:265820 Radder JE, et al., Variable Susceptibility to Cigarette Smoke-Induced Emphysema in 34 Inbred Strains of Mice Implicates Abi3bp in Emphysema Susceptibility. Am J Respir Cell Mol Biol. 2017 Sep;57(3):367-375
All:  1 reference(s)

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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