The marks glyph is set below the baseline. Open the particular glyph in any font editor and move it a bit upward.

Soroush, you need to work with WinAscent and WinDescent. If you contact me offline I can send you an e-mail with a more detailed explanation.

Frode, Thanks. I try to overcome by setting WinDescent to -1500 but it increases line-spacing. is there another way to do without changing line spaces?

with very big spaces between lines:

This is indeed a metrics problem. There are a couple of ways to address it.

1) A work around in MS Word: set linespacing to be an exact amount rather than relative to default spacing. This usually prevents clipping.

2) Set the OS/2 Win values to be large enough to accomodate the marks, but leave the OS/2 Typo values as you would like them to be to define default linespacing. Then use a table editor to a) set the OS/2 table version to 4 and b) turn on fsSelection bit 7. This bit tells an application to use the Typo metrics for linespacing instead of the Win values. The caveats with this approach are that not all applications support this bit setting, so linespacing may be inconsistent, and MS Word does some heuristics to avoid clipping that sometimes override the Typo values.