AN LGT ACR CREW CLBED THROUGH ITS ASSIGNED ALT ON DEP. THEIR PRE-DEP CLRNC AMENDED THE ALT THAT WAS PUBLISHED ON THE NEWARK 4 SID.

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THE PRE-DEP CLRNC (PDC) WAS DELIVERED TO THE COCKPIT JUST PRIOR TO PUSHBACK. THE FO SET THE TRANSPONDER CODE AND ALT ALERT PER THE EWR 4 DEP (5000 FT). AFTER TKOF ON 22L; EWR TWR ADVISED 'CONTACT NY DEP 119.2.' THE FO WAS FLYING; I WAS HANDLING COMS. I CALLED NY DEP AND RPTED LEAVING 1800 FT. PASSING 2500 FT; NY DEP SAID 'MAINTAIN 2500.' I SAID 'WE ARE THROUGH 2500; WE'LL GO BACK DOWN.' THE PEAK ALT I SAW WAS 2900. NY DEP SAID; 'DIDN'T THE TWR GIVE YOU 2500?' I SAID; 'NO; THE PDC SAID 5000 AND THAT'S WHERE WE WERE GOING.' AFTER HESITATING A MOMENT; NY DEP INSTRUCTED US TO TURN TO 310 DEGS/CLB TO 10000. NOTHING ELSE WAS SAID AND DEP HANDED US OFF TO ANOTHER FREQ. LEAVING 10000 AND PROCEEDING ON COURSE; I CHKED THE PDC; AND IT DID IN FACT SAY NEWARK 4 DEP...'EXCEPT' MAINTAIN 2500. BOTH THE FO AND I MISSED SEEING THE 'EXCEPTION' TO THE PUBLISHED SID. REF CORRECTIVE ACTION -- I SUGGEST ANY AMENDMENT OR EXCEPTION TO THE SID BE HANDLED AS WX OR TFC RERTES ARE HANDLED; I.E.; -- PDC SHOULD BE SUSPENDED AND A CONTACT TO CLRNC DELIVERY BE MADE FOR A READING OF THE CLRNC AND A READBACK BE MADE. NEWARK APPEARS TO BE ESPECIALLY BAD ABOUT CHANGING THE CLRNC. PRIOR TO INITIATING THE PDC PROC; I HAVE RECEIVED THE EWR 4 DEP FROM CLRNC DELIVERY WHICH STATES 5000 FT. TAXIING OUT GET 2500 FROM GND CTL; AND THE 'MAINTAIN 5000' ON EWR 4 FROM THE TWR WHEN TOLD TO 'TAXI INTO POS AND HOLD' -- THEN 'CLRED FOR TKOF; MAINTAIN 2500.' AFTER TKOF; I'VE BEEN TEMPTED TO ASK 'HAVE YOU CHANGED YOUR MIND AGAIN.' CONFUSING TO SAY THE LEAST. SUPPLEMENTAL INFO FROM ACN 226381: I INADVERTENTLY OVERLOOKED THE AMENDED ALT OF 2500 FT ON THE NEWARK 4 SID ON THE PDC. TO AID IN PREVENTING A RECURRENCE; THE USE OF PDC'S THAT H AVE EXCEPTIONS TO EITHER ALTS AND/OR RTE CHANGES SHOULD EITHER BE SUSPENDED AND A FORMAL READBACK OF THE AMENDED PORTION BE GIVEN BY CLRNC DELIVERY OR THE FORMAT OF THE PDC SHOULD BE ALTERED SO AS TO 'FLAG' ANY CHANGE TO A STANDARD PRINTED PROC. UNDER THE CURRENT SYS; IT'S EASY TO MISS AN EXCEPTION.