Date: 201808
Local time of day: 1801-2400
Location: ZZZ.Airport, US
Flight conditions: IMC
Light: Night
Aircraft: B737 Undifferentiated or Other Model
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Mission: Passenger
Flight phase: Climb
Airspace: Class B ZZZ
ATC / advisory: TRACON ZZZ
Reporter organization: Air Carrier
Reporter function: First Officer; Pilot Not Flying
Reporter qualification: Flight Crew Instrument; Flight Crew Air Transport Pilot (ATP); Flight Crew Multiengine
Human factors: Situational Awareness; Human-Machine Interface
Second reporter function: Pilot Flying; Captain
Anomaly: Aircraft Equipment Problem Less Severe; Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Clearance
Detector: Person Air Traffic Control; Person Flight Crew
When detected: In-flight
Result: Air Traffic Control Issued Advisory / Alert; Flight Crew Became Reoriented; Flight Crew FLC Overrode Automation
Contributing factors: Aircraft; Human Factors
Primary problem: Human Factors

Narrative: While climbing out of ZZZ on the RNAV departure; just as we passed the ZZZZZ intersection; the aircraft began to turn towards the next fix in the sequence. I am not sure if ZZZZZ1 was actually in the FMC at the time or not; but shortly after we began our turn; ATC told us that it looked like we missed ZZZZZ1 by about 6 miles. Still in the turn; I looked down at the FMC and saw that our previous fix showed ZZZZZ with ZZZZZ3 as the fix we were turning towards. The departure calls for ZZZZZ. ZZZZZ1. ZZZZZ2. ZZZZZ3. I replied with it looks like our previous fix was ZZZZZ and we are turning towards ZZZZZ3. The controller said we should be going to ZZZZZ1; but that it was OK. He instructed us to just go direct to ZZZZZ3. There was no further issue.I loaded the FMC with what was on our [flight plan]; prior to receiving our clearance. When I input the departure; I selected runway XXR then the departure then the transition. I checked the route for discontinuities; but I did not check each point on the departure. When we received our clearance from the FMC ATC feature; there was a new route prompt; but the route was the same that we were filed. The Captain selected the load feature from the FMC and had to reload the departure. He said that he did it the same way that I did; but this happened during my walk around. I did review the clearance in the CPDLC (Controller pilot Datalink Communications) and saw that the new route was actually our filed route.I am kind of at a loss as to how this can happen; given that we loaded it the way we always do. Obviously; had I checked each individual fix; I would have caught the problem. If we load the departure from the FMC correctly; I don't see how 2 fixes end up missing. We would have to physically delete them. If there were a discontinuity; and we closed it incorrectly; in this case it should have also deleted ZZZZZ3. That was not the case. ZZZZZ1 was a bypass fix on our departure and the turn was pretty significant; but even if the FMC sequenced an early turn; we should have seen ZZZZZ1 or ZZZZZ2 as our previous fix. It bothers me because I feel like the route was loaded the way we always load routes. I just want to be sure that it is not some FMC issue causing this to happen.There was an [company bulletin] that specifically said the 737 is now authorized to do this departure.


Second narrative: We received a revised ATC clearance via CPDCL (Controller pilot Datalink Communications). It was accepted and loaded. I reloaded the runway; SID and transition. I then closed the discontinuity. The route was then checked. ZZZZZ.ZZZZZ3 flight plan was loaded. On climbout passing ZZZZZ the aircraft turned direct ZZZZZ3. ATC informed us that we turned prior to ZZZZZ1. There was no separation lost and then ATC cleared us direct ZZZZZ3. The ZZZZZ1 and ZZZZZ2 waypoints did not sequence to the LEGS page. I did not confirm the next waypoint while flying the SID during climbout; so I do not know when the waypoints dropped out.


Synopsis: B737 flight crew reported a Course Deviation due to several waypoints dropping out of the FMC after CPDLC clearance revision.