Document:

Prepared by R.R. Donnelley Financial -- EX-10.1

 Exhibit 10.1 

Addendum #3 
 To The Lease 

By and Between Condiotti Enterprises, Inc. (“Lessor”) 

And 
 Ultragenyx Pharmaceutical,
Inc. (“Lessee”) 
 Dated on or about July 1, 2011 

Lessor and Lessee are parties to that certain Lakepoint Business Park Standard Lease dated on or about July 1, 2011 and amended by that certain Addendum
One dated on or about July 1, 2011 and that certain Addendum Two dated on or about March 7, 2012, which together constitute the Lease and pursuant to which Lessee leases from Lessor certain space on the first and second floors of the
Building located at 60 Leveroni Court, Novato, California. 
 Now, therefore, the parties do wish to amend the Lease further as follows: 

56. There shall be added to the existing Premises occupied by Lessee (20,490sf consisting of 18,097sf second floor and 1,809sf “Load Factor”,
and 574sf first floor warehouse as detailed in Addendum Two, together the “Existing Space”) approximately 24,846sf of first floor space (the “Expansion Space”), bringing the total space occupied by Lessee to 43,517±sf,
exclusive of the Load Factor as addressed in Section 61 below (the “Entire Premises”) which Entire Premises comprises the entire Building located at 60 Leveroni Court, Novato, California. The square footage of both the Existing Space
and the Expansion Space shall be verified by Lessor prior to occupancy and to BOMA standards. The architectural footprint drawings produced by Lessor’s architect shall be attached to this Addendum #3 as exhibit H. 

57. The Term for the Expansion Space shall commence on May 1, 2014 and expire on April 30, 2019, unless extended as provided hereunder. 

58. The Term for the Existing Space shall be extended to be co-terminous with the Expansion Space, so that the Term for the Entire Premises shall expire
on April 30, 2019, unless extended as provided hereunder. 
 59. The Anniversary Date for the Entire Space shall be extended to May 1st for
the purposes of the annual Base Monthly Rent increase and the annual reduction in value for the Letter of Credit (the “LOC”), subject to the terms of the Lease. 

60. Base Monthly Rent for the Existing Space shall be increased to $25,122.11 effective May 1, 2014. This amount shall be inclusive of the 2014
annual Base Monthly Rent increase which had been scheduled for March 1, 2014. 

 61. Effective May 1, 2014 Base Monthly Rent for the Expansion Space shall be $28,407.87, (inclusive
of a credit for the removal of the Load Factor space as indicated above), bringing the total Base Monthly Rent for the Premises as of May 1, 2014 to $53,529.98. 

62. Thereafter, Base Monthly Rent for the Entire Space shall be increased annually, effective May 1 of each year, in accordance with the terms of
the Lease. 
 63. Section 50 of the Lease is no longer applicable and is hereby deleted. 

64. Base Monthly Rent for the Expansion Space shall be waived by Lessor for the month of May, 2014 as a one-time concession. Lessee remains responsible
for the timely payment of Operating Expenses as provided in the Lease. 
 65. Lessee intends to install substantial improvements to the Expansion
Space at Lessee’s sole cost and expense. In this regard Lessee shall present Lessor with detailed specifications and budget for Lessor’s review and approval, denial, or modification, prior to the start of any work on the premises.
Lessor’s approval of the proposed improvements shall not be unreasonably withheld, conditioned or delayed. 
 66. Once the improvement budget and
designs have been approved by Lessor, Lessee shall post a completion bond for the benefit of Lessor and in an amount sufficient to cover all of the proposed improvements. Such bond may be drawn on by Lessor in the event of Lessee’s failure to
complete or pay for the approved improvements and/or to restore the Premises to rentable condition in the event that Lessee abandons or fails to complete the project. 

67. Upon Lessor’s approval of the improvement designs and budget and further upon Lessee providing Lessor with the above mentioned completion bond
and Lessee’s insurance extending to cover the Expansion Space, Lessor shall grant Lessee access to the Expansion Space for the diligent pursuit of completion of the approved improvements. Lessee shall not incur Base Monthly Rent for this period
of early access until May 1, 2014 as stated above, but shall remain responsible for the prompt and timely payment of all utilities and other expenses incurred in connection with the early access to the Expansion Space including Operating
Expenses as detailed in Section 9 of the Lease. 
 68. Lessee’s build-out of the Expansion Space shall be subject to the Terms of the Lease
including, but not limited to, Lessor’s right to review and approve, deny, or modify any and all change orders to the designs, budget, and plans as originally approved by Lessor. 

69. Lessor shall provide Lessee with an improvement contribution not to exceed $368,592.00 (“Lessor’s Contribution”). Such contribution
shall be available for improvements to the Expansion Space only, and shall be subject to the following: 
 a.) Lessee shall not cause or
allow any lien(s) to be placed upon the Property in relation to the improvements to be constructed by Lessee and shall promptly remove any liens. In all representations to the subcontractor(s), general contractor, material and/or labor suppliers or
others Lessee shall characterize Lessor as a “Non-participating Lessor” and shall hold and keep Lessor harmless from any and all liens, legal actions, and damages of any kind resulting from Lessee’s build-out activities on the
Property. 

 b.) Lessee shall post an increase in the LOC to include the amount of Lessor’s Contribution
to the improvements. 
 c.) Lessee shall submit to Lessor copies of all invoices and conditional lien releases as they are acquired
throughout the build-out. 
 d.) No part of Lessor’s Improvement Contribution shall be used for the acquisition or installation of
Lessee’s personal property. 
 e.) Promptly upon receipt of all unconditional lien releases, a copy of the final signed-off permits, and
a complete set of “As-Built” plans Lessor shall pay up to the improvement contribution amount to Lessee. Also at this time, Lessor shall endorse documents necessary to release the completion bond or so much of it as shall remain. 

70. Lessee shall increase the LOC in an amount equal to Lessor’s maximum Contribution to $594,192.00 (“Increased Letter Of Credit”) upon
execution of this Addendum 3. Subject to the Terms of the Lease and Lessee’s addition of the amount of Lessor’s maximum Contribution amount, the annual amount available for reduction for May, 2014 shall be $75,200.00. Thereafter and
continuing to be subject to the Terms of the Lease the annual available LOC reduction amount shall be one-fifth of the remaining LOC amount throughout the revised Term of the Lease, but in no event shall the LOC be reduced to less than $75,200.00
throughout the revised initial Lease Term. 
 71. Lessor shall deliver the Expansion Space with all Building Systems in good working condition prior
to Lessee’s early access to the Expansion Space. 
 72. Subject to Lessor’s measurement of the space as mentioned in Section 56 above,
Lessee shall have exclusive use of up to 111 unreserved and unassigned parking spaces on the property. 
 73. Lessor has provided Lessee with a
subordination, non-disturbance and attornment agreement (the “SNDA”) from Lessor’s current lender, to be executed simultaneously with this Addendum 3. The SNDA shall provide that Lessee shall have the right to occupy the Premises
pursuant to this Lease so long as Lessee is not in default hereunder beyond any applicable notice and cure period. Lessor shall submit the executed SNDA to any and all superior mortgagees and, upon receipt of the fully executed SNDA from Mortgagee,
shall provide Lessee with a copy and shall attach the original to this Addendum #3 as Exhibit “I”. 
 74. Throughout the revised Initial
Term of this Lease, Lessee shall have a right of first offer (the “Right of First Offer”) with respect to the space at 52 Leveroni Court, Novato, California from time to time which is or will become vacant. Lessee shall have twenty-one
(21) days to respond to Lessor’s written notice to Lessee to lease any space that is within Lessee’s Right of First Offer. 
 Any space so
leased by Lessee pursuant to the Right of First Offer shall be subject to all of the terms and conditions of this Lease including, without limitation, the Term, rate of Base Monthly Rent, and a $16.00 per square foot improvement allowance for
constructing improvements said space. Should Lessee exercise this Right of First Offer the Lease Term shall be extended to be not less than sixty (60) full months from commencement of the Right of First Offer space and shall include the Entire
Premises at 60 Leveroni Court, Novato, California. 

 Each party agrees to bear the costs of any commissions incurred in the addition of such space. 

75. Except as expressly modified by this Addendum #3 the Lease shall remain in full force and effect. 

Agreed to this 12th day of February, 2014. 
  

					
	Lessee	 		 	Lessor
			
	/s/ Tom Kassberg	 		 	/s/ Jan Warz
	Tom Kassberg, Chief Business Officer	 		 	Jan Warz, Vice President and COO
			
	Ultragenyx Pharmaceuticals, Inc.	 		 	Condiotti Enterprises, Inc.EX-4.1

 Exhibit 4.1 
  

 

 THE CORPORATION IS AUTHORIZED TO ISSUE TWO CLASSES OF STOCK, COMMON STOCK AND PREFERRED STOCK. THE BOARD OF
DIRECTORS OF THE CORPORATION HAS AUTHORITY TO FIX THE NUMBER OF SHARES AND THE DESIGNATION OF ANY SERIES OF PREFERRED STOCK AND TO DETERMINE OR ALTER THE RIGHTS, PREFERENCES, PRIVILEGES AND RESTRICTIONS GRANTED TO OR IMPOSED UPON ANY UNISSUED SHARES
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 THE CORPORATION SHALL FURNISH WITHOUT CHARGE TO EACH STOCKHOLDER WHO SO REQUESTS A STATEMENT OF THE POWERS, DESIGNATIONS, PREFERENCES
AND RELATIVE, PARTICIPATING, OPTIONAL OR OTHER SPECIAL RIGHTS OF EACH CLASS OF STOCK OF THE CORPORATION OR SERIES THEREOF AND THE QUALIFICATIONS, LIMITATIONS OR RESTRICTIONS OF SUCH PREFERENCES AND/OR RIGHTS. SUCH REQUESTS SHALL BE MADE TO THE
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	The following abbreviations, when used in the inscription on the face of this certificate, shall be construed as though they were written out in full according to applicable laws or regulations:
			
	TEN COM	  	–   as tenants in common	  	UTMA –                     Custodian            
         
		  		  	                      (Cust)               
          (Minor)
	TEN ENT	  	–   as tenants by entireties	  	under Uniform Transfers to Minors
			
	JT TEN	  	–   as joint tenants with right of survivorship	  	Act
                                         
                       
		  	     and not as tenants in common	  	        (State)
	Additional abbreviations may also be used though not in the above list.

  
  

			
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                             Shares of the capital stock represented by the within Certificate, and do
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appoint                                        
                                         
                                         
               Attorney to transfer the said stock on the books of the within-named Corporation with full power of substitution in the premises. 

 

							
	Dated	 	 	 		  	 
				
		 		 		  	 
				
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