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Page 24 of Publication 4164:

The superseding return designation is available for Forms 1041, 1120, 1120-F, 1120-S and 1065. The superseding return designation is not available for Forms 990, 990-EZ, 990-PF, 1040, 1120-POL and 2290. The amended return box must be checked for any subsequent Forms 990, 990-EZ, 990-PF or 1120-POL returns to be accepted.

https://www.irs.gov/pub/irs-pdf/p4164.pdf

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