You will have pay Zakat on the total value of the portfolio. For example, the shares that you own in company X are valued at £1000 on your Zakat anniversary date, you will pay Zakat at 2.5% on this value i.e. £25.
Remember your Zakat in due on how much the shares is worth on your Zakat anniversary date.

After selling the share, the proceeds will be liable for Zakat if you still own these funds on your Zakat anniversary.
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