Retirement tax questions

I read that SEP-IRA contributions are not subject to:

  • Federal income taxes, or
  • Social security and Medicare taxes
  • FUTA tax

Does this mean I subtract the amount of the SEP IRA contribution from taxable wages on Form 941 and 940? So that would mean at the end of the year box 1 stays the same on the W-2 but box 3 & 5 end up being lower because of SEP IRA contribution?