When the option to submit your VAT return to HMRC is missing, you'll have to make sure that the Making Tax Digital option is enabled in the settings. This is to help authorise QuickBooks to interact with HMRC.
Here's how:
Go to the Gear > Account and settings.
On the left panel, click Advanced.
In the Making Tax Digital section, click the Learn how to connect button.
Follow the on-screen instructions.
I've got this sample screenshot for a visual reference:
Once you have completed the process, you can start submitting your VAT return through QuickBooks.