Given the amount, I would just double-up next quarter. There will be no red flags in the IRS system just because you skipped a payment. If anything, you may owe them a little bit of interest for the time period you were underpaid (can file form 2210 with your return, or let the IRS calculate it themselves). If the true amount due quarterly is < 1,000, the total interest owed would be < $10 (1,000 * 3% current underpayment rate * .25 (3 months / 12)).