Air carrier flight crew reported a terrain alert from ATC during their departure while flying the SID. The pilots stated that one of the fly over fixes dropped from the FMS causing the aircraft to fly a shorter distance to the next further out fix. This caused the 'too low' event from ATC.
Synopsis
Air carrier flight crew reported a terrain alert from ATC during their departure while flying the SID. The pilots stated that one of the fly over fixes dropped from the FMS causing the aircraft to fly a shorter distance to the next further out fix. This caused the 'too low' event from ATC.
Narrative
First Officer (FO) programmed FMC. Once the CPDLC was downloaded; there was a load new route prompt. FO loaded the new route clearance; verified it then executed the new clearance. It was the FO's leg to ZZZ1. I gave the Captain's Brief; then he gave the clearance briefing. We reviewed the CPDLC clearance and verified the new route entered into the FMC was the same as given in the new route clearance. After reviewing the clearance and verifying it was correct he briefed the LEGS page and I verified it on the departure chart. We completed the remaining briefs and checklists. We taxied to [Runway] XXL and took off. There was a temporary confusion and set speed was called for and executed before 7400 ft. MSL. I identified it and continue the climb to 7400 ft. MSL; before cleaning up. Tower switched us over to Departure; about 7400 ft. MSL. On initial contact; Departure gave us a Low Altitude Alert and we expedited climb. At that time; I realized that after passing ZZZZZ we went direct ZZZZZ1 bypassing ZZZZZ2; putting us east of the departure. Departure gave us a number to call for possible deviation. We completed the flight to ZZZ1. En route; we reviewed the CPDLC; route; departure; everything trying to figure out what happened. The FO even had highlighted the departure route on his chart. We briefed everything as we should and verified it. We could not conclude how the fix ZZZZZ2 was bypassed. The next morning; I contacted (name) Company ATC specialist; explained the situation. He called TRACON about the event.Watch and verify each fix on the route as your flying it. This was a first for me. I am very deliberate about verifying and briefing clearances.Aircraft went from ZZZZZ direct ZZZZZ1 by passing ZZZZZ2 fix.
Second reporter narrative
I was operating Flight #XXXX out of ZZZ to ZZZ1 as the pilot flying (PF); on the evening of (date) when Air Traffic Control advised us of a possible deviation on departure. During our normal preflight duties; while programming the FMC at the gate in ZZZ; I had received our Company filed flight plan through the ACARS system. This flight plan had us filed to the ZZZ1 Airport that evening via ZZZ ZZZZZ2 3 ZZZZZ2..ZZZZZ3..ZZZZZ4..ZZZZZ5 ZZZZZ6 2 ZZZ1; departing off Runway XXL. This 'Company filed' flight plan was loaded into the box and reviewed. Shortly thereafter; I received our ATC clearance request through CPDLC. The clearance that was received from CPDLC was a 'new' route that was different from the Company route; previously entered in the FMC and now cleared us to the ZZZ1 Airport via ZZZ ZZZZZ7.ZZZZZ1 ZZZZZ5.ZZZZZ2 ZZZ1. This new flight plan was acknowledged and I entered it into the FMC using the 'LOAD' prompt function on the ATC UPLINK clearance page.The Captain and I then went about our normal preflight duties preparing for the flight. We spent a considerable amount of time briefing and talking about the 'Complex single engine escape maneuver' for the departure on Runway XXL and the high terrain in the surrounding area. We then set up the radios and map accordingly for the escape maneuver. We reviewed the new clearance and the points on the departure against the Jepp chart and FMC LEGS page and completed all checklist. After takeoff and while following the guidance of the flight director; I began a left turn toward ZZZ1 to the ZZZZZ1 fix on the flight plan route. Shortly thereafter the Air Traffic Controller then advised us of a 'Low Altitude and Terrain Alert' in our area. He stated that we had 'rising terrain in the area and suggested we increase our rate of climb;' which I did promptly per his instructions. At this time; I was a little perplexed by the Controllers 'Terrain Alert' announcement since we were on an instrument departure and it was the same flight plan; I loaded via the 'LOAD' prompt function received by ATC. The Captain then asked the controller if he showed us direct to the ZZZZZ1 waypoint; per the flight plan and he said 'Yes'. The Controller then stated that we turned to ZZZZZ1 a little early and should have made the turn in another couple of miles. At the time of departure; both the Multifunction Flight Displays (MFD's) in the cockpit were displaying the 'Terrain' function for takeoff and remained on for the entire duration of the flight. At no time during the departure did the MFD displays show a 'YELLOW' caution; or a 'RED' Warning for terrain in our flight path; nor did we get any GPWS aural warnings of any kind. The terrain displayed on the MFD remained GREEN on departure and for the entire duration of the flight to ZZZ1. The remainder of the flight was completed uneventfully.I feel like a SID transition selection may have been missed while loading the FMC using the prompt function from the ATC clearance page; causing a early turn over rising terrain. I feel; had the Controller stated 'On departure RNAV (a certain fix)' This may have alerted me to any errors in the box; or fixes that may have been missing to prevent such a turn.Controller advised us of high terrain in our area and suggested we climb.
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Source: NASA Aviation Safety Reporting System (public domain). Reports are voluntary submissions and are not verified by NASA.