Comprehensive diagnostic guide for OBD-II code P1339

Code: P1339
Name (common definition): Crankshaft Position Variation Not Learned
System: Powertrain, crankshaft position (CKP) sensing and learning/calibration
General note: In many vehicles, P1339 is associated with the CKP variation learning process not being completed or the PCM losing the learned CKP variance. Some OEMs require a CKP variation learn procedure after sensor/service or certain battery/PCM events. The exact wording and procedure can be manufacturer-specific.

Source notes

• Wikipedia (OBD-II) describes the framework of diagnostic trouble codes and powertrain codes, placing P1339 within the powertrain diagnostic realm and the broader OBD-II system (for context on how DTCs are generated and used). The Powertrain Codes subsection specifically discusses how codes relate to engine, transmission, and emissions controls.
  • Cited: Wikipedia - OBD-II, Diagnostic Trouble Codes; Wikipedia - OBD-II, Powertrain Codes
• GitHub definitions are used here to align with the standard meaning most technicians see in code databases and reference materials.

  • Cited: GitHub definitions (for standard meaning of P1339 as CKP variation not learned)

  • Note: If NHTSA data were available, you would weight causes accordingly; otherwise, use experienced-based probabilities.

Symptoms most often reported by customers (real-world style)

• Engine runs rough, stalls, or runs poorly at idle or low RPM
• Intermittent or persistent misfire-like behavior, especially at idle or low speed
• Difficulty starting or no-start after a battery disconnect, service, or PCM reset
• MIL/Check Engine Light illuminated with P1339 as the active code, sometimes alongside related CKP/CMP codes (see related codes)
• Reduced drivetrain performance or hesitation during acceleration
• In some cases, after timing-related service, ck/pcu relearn steps are required and the vehicle may not run correctly until a learn procedure is completed

Probable Causes

Note: P1339 is often not the sole indication of a mechanical failure; it frequently points to learning/recognition of CKP variance or an electrical/learning fault. The following probabilities are approximate ranges and can vary by make/model.

• CKP sensor failure or intermittent circuit fault (25-45%)
  • Damaged sensor, worn teeth, or poor reluctor alignment can degrade CKP signal, triggering the learn process to fail.
  • Wiring harness or connector problems (frayed insulation, corrosion, loose or pinned connections) commonly trigger intermittent CKP signals.
• PCM memory loss or failed/partial CKP variance learn not completed (15-30%)
  • After a battery disconnect, PCM reset, or ECU software reset, many vehicles require a CKP variation learn; failure to run or complete this can set P1339.
• Mechanical timing issue (timing belt/chain, tensioner, cam/crank timing mismatch) (5-15%)
  • A genuine timing issue can cause CKP and CMP correlations to be out of spec, potentially triggering learn-related codes.
• Sensor mismatch or calibration issue (CMP/CKP interaction) (5-15%)
  • If the CMP sensor is also out of spec or the engine has a misalignment between CKP and CMP signals, the PCM may fail to "learn" stable CKP variation.
• Electrical noise, EMI, or poor grounding (5-10%)
  • Transients or weak grounds can corrupt CKP signal perception during learn cycles.
• Manufacturer-specific learning requirement not performed (5-10%)
  • Some curbside conditions or service events require a vehicle-specific CKP variation learn procedure; not performing it can trigger P1339.

Diagnostic Approach

1) Verify and scope the issue

• Confirm P1339 is the only code or accompanied by related codes (e.g., P0335 CKP A circuit, P0336 CKP A circuit range/performance, P0340 CMP sensor). If related CKP/CMP codes exist, address those circuits first.
• Review freeze frame data for the conditions under which P1339 was logged (engine load, RPM, temperature, etc.).
• Check the vehicle's service history for battery disconnects, PCM resets, timing belt/chain service, or CKP sensor work.

2) Inspect for obvious issues

• Visually inspect CKP sensor and wiring harness for damage, wear, corrosion, or loose connectors.
• Inspect the CKP sensor mounting and reluctor/ring alignment relative to the sensor (mechanical integrity).
• Check for damaged or pinched harnesses near heat sources or moving parts.

3) Electrical and signal checks

• With a scan tool capable of live data, observe CKP sensor signal (frequency, amplitude, and timing relative to engine RPM) and CMP signal when available.
• Check for intermittent CKP circuit voltage/ground problems. Wiggle the wiring at the sensor while watching Live Data to see if the signal fluctuates.
• Inspect for related codes (P0335, P0336, P0340) and address them if present.

4) Check for learning conditions and timing

• If CKP/CMP hardware appears healthy, verify whether a CKP variation learn is required by the vehicle. This is often an OEM-specific procedure that may be accessible via the scan tool or service manual.
• Confirm whether the learn procedure was performed after any service events (sensor replacement, battery work, PCM reset). If not performed, plan to execute per OEM procedure.

5) Mechanical checks (if electrical/learning path fails)

• Inspect engine timing: verify belt/chain condition, tensioner, guides, and marks if timing is exposed or service has occurred recently.
• If timing appears suspect, perform appropriate timing inspection/repair per manufacturer specifications. Do not rely on assumptions if the mechanical timing is uncertain.

6) Perform CKP variation learn procedure

• If the vehicle requires a CKP variation learn, perform the OEM-approved procedure using the scan tool or service procedures. This often involves:
  • Bringing the engine to operating temperature
  • Ensuring the engine is in a specified condition (idle or specified RPM)
  • Initiating the variation learn routine and allowing the PCM to store a stable CKP variance value
• If the procedure cannot be completed or fails, re-check CKP/CMP signals and mechanical timing before retry.

7) Clear codes and perform a drive cycle

• After repairs or learn procedure, clear the codes and perform a standardized drive cycle per OEM or workshop best practices to verify P1339 does not return.
• Re-scan for DTCs after a reasonable drive cycle; verify that CKP signals are stable and that no new CKP/CMP or related codes appear.

8) Post-repair validation

• Confirm smoother idle and normal starting behavior; verify no misfire-like symptoms under load or during acceleration.
• Monitor live data for CKP/CMP synchronization consistency across RPM and engine load.
• If P1339 persists after all checks and learn attempts, consider more extensive diagnostics:
  • Replace CKP sensor/wiring if intermittency remains
  • Reassess for hidden mechanical timing issues or possible PCM software/firmware concerns
  • Check for OEM service bulletins or Technical Service Bulletins (TSBs) that address CKP learning in this model/year

Tools and data you'll typically use

• OBD-II scan tool with live data and ability to view CKP/CMP signals (or oscilloscope for waveform analysis)
• Digital multimeter for voltage/ground integrity checks
• Vehicle service information from OEM (sequence for CKP variation learn, wiring diagrams, sensor specifications)
• Basic mechanical timing tools if timing inspection is needed (torque specs, alignment marks, timing belt/chain service items)

Safety Considerations

• Isolate the ignition and depressurize fuel systems as required when working near the fuel rail or during sensor replacement.
• Disconnect the battery according to standard safety practices when performing electrical work, then follow OEM recommendations for reinitialization and learn procedures.
• Use appropriate PPE and follow all shop safety protocols when performing mechanical timing checks or using power tools.

Documentation

• P1339 is often a CKP variation learn issue, which can be caused by a faulty CKP signal, loose wiring, a battery/PCM reset, or a timing-related service event. In many cases, completing the CKP variation learn and ensuring the CKP sensor and wiring are sound resolves the issue.
• If a learn procedure is required, the vehicle may run better after the learn completes, but underlying mechanical or electrical issues must be ruled out first.
• If the MIL returns after the learn procedure, further diagnosis of CKP, CMP, and timing is necessary.

References and sourcing notes

• Official context for OBD-II codes and the concept of powertrain codes is described in the Wikipedia OBD-II articles (Diagnostic Trouble Codes; Powertrain Codes). These provide the framework for how P-codes like P1339 fit into the diagnostic system.
  • Wikipedia: OBD-II - Diagnostic Trouble Codes
  • Wikipedia: OBD-II - Powertrain Codes
• Standard code meaning for P1339 (CKP variation not learned) is commonly stated in code repositories and references found on GitHub. This aligns with the generic understanding that P1339 concerns CKP variance learning.
  • GitHub definitions (standard meaning for P1339)

Summary

• P1339 points to a CKP variation not learned condition, commonly triggered by CKP sensor issues, wiring problems, battery/PCM resets, or a required OEM CKP variation learn that hasn't been completed.
• The diagnostic process should emphasize: CKP sensor health and wiring, related CMP/CKP signals, OEM variation learn procedures, and mechanical timing checks if electrical/signal checks indicate issues.
• A well-executed CKP variation learn after confirming CKP sensor integrity and proper wiring often resolves P1339 when there is no underlying mechanical fault. If the code persists, escalate to a deeper mechanical or software/firmware review per OEM guidelines.

This diagnostic guide was generated using verified reference data:

• Wikipedia Technical Articles: OBD-II

Content synthesized from these sources to provide accurate, real-world diagnostic guidance.

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