Do you know… how to find viability data in the IMPC portal?

Some genes are classified by the IMPC as having a preweaning lethality phenotype. Can you identify the results on the gene page that lead us to conclude a gene results in a preweaning lethality phenotype? 

Answer:

The IMPC conducts a Viability procedure to understand how essential a gene is. Depending on the gene that is knocked out, null homozygous mouse strains may be viable or not.

Heterozygotes individuals for the null allele are crossed with each other and the observed ratios of wildtype, heterozygous and homozygous individuals are compared to the expected Mendelian ratios. This enables to associate genes with a “Viable”, “Subviable” or “Lethal” phenotype:

Tmem63b displays a preweaning lethality phenotype.

There are a number of ways in which we can find the results for the Viability procedure:

• The phenogrid symbol for mortality/aging is orange. Hovering over the icon, the message “mortality/aging: significant” is displayed
• In the Significant phenotypes table, the phenotype “preweaning lethality, complete penetrance” is displayed

You can click on “Viability Data” link on the left in the header of the page (Figure 35) or, alternatively, the corresponding row in the table. You will access the chart page for Viability and view the details of the experiment performed, the data collected and the statistical analysis conducted.

NOTE THAT… In the absence of homozygote pups that are viable, the heterozygotes mice will enter the adult phenotyping pipeline, while the embryos will undergo an embryonic assessment that intends to determine the defects that take place during development. The column “Zygosity” shows that, except for the phenotype “preweaning lethality”, all other phenotypes displayed here are for heterozygotes.