EX-4.6





 Exhibit 4.6 

Execution Version 

PROGENITY, INC. 

AMENDMENT NO. 1 TO 

FOURTH AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT 

November 10, 2020 
 This
Amendment No. 1 (this “Amendment”) to that certain Fourth Amended and Restated Investors’ Rights Agreement, dated as of August 27, 2019 (the “Agreement”), by and among Progenity, Inc., a Delaware
corporation (the “Company”), the investors listed on Exhibit A thereto (each, an “Investor” and collectively, the “Investors”), and the holders of Common Stock listed on Exhibit B thereto.
Capitalized terms used in this Amendment that are not otherwise defined herein shall have the respective meanings assigned to them in the Agreement. 

RECITALS 
 WHEREAS,
the Company and the Investors desire to amend the Agreement as set forth below; 
 WHEREAS, the undersigned Investors represent the
holders of a majority of the Registrable Securities outstanding on the date of this Amendment and, as such, together with the Company, have the right, power and authority pursuant to Section 4.4 of the Agreement to execute
and deliver this Amendment and amend the Agreement in the manner provided herein. 
 NOW, THEREFORE, in consideration of the mutual
promises and covenants contained in this Amendment and other good and valuable consideration, the receipt and adequacy of which are hereby acknowledged, the parties hereto agree as follows: 

AGREEMENT 
  

	1.    The	 following defined term on Section 1(a)(xv) of the Agreement is hereby deleted in its entirety and
replaced with the following: 


 “Registrable Securities” means (i) the shares of
Common Stock issuable or issued upon conversion of the Preferred Stock, including any shares of Common Stock issued on or before the date hereof, upon conversion of preferred stock of the Company outstanding at any time, other than shares for which
registration rights have terminated pursuant to Section 2.15 hereof, (ii) the shares of Common Stock issued pursuant to the Common Stock Purchase Agreement, dated as of August 8, 2016, by and between the Company and BCI, other than shares
for which registration rights have terminated pursuant to Section 2.15 hereof, (iii) the shares of Common Stock issuable or issued upon conversion of the Warrant Shares (or, following a Qualified IPO, issuable upon exercise of the
Warrant), other than shares for which registration rights have terminated pursuant to Section 2.15 hereof; (iv) any other shares of Common Stock issued as (or issuable upon the conversion or exercise of any warrant, right or other security
which is issued as) a dividend or other distribution with respect to, or in exchange for or in replacement of, the shares listed in clauses (i) through (iii) and clause (v); and (v) shares of Common Stock issuable or issued upon the
conversion of the Unsecured Convertible Promissory Note dated May 8, 2020, issued to Athyrium Opportunities 2020 LP; provided, however, that the foregoing definition shall 

  
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 Execution Version 

exclude in all cases any Registrable Securities sold by a Person in a transaction in which such Person’s rights under
this Agreement are not assigned. Notwithstanding the foregoing, such shares of Common Stock shall only be treated as Registrable Securities if and so long as (A) they have not been sold to or through a broker or dealer or underwriter in a
public distribution or a public securities transaction, (B) they have not been sold in a transaction exempt from the registration and prospectus delivery requirements of the Securities Act under Section 4(a)(1) or Rule 144 thereof so that
all transfer restrictions, and restrictive legends with respect thereto, if any, are removed upon the consummation of such sale, and (C) the Holder thereof is entitled to exercise any right provided in Section 2 in accordance with
Section 2.15 below. 
  

	2.	 This Amendment may be executed in two or more counterparts, each of which shall be deemed an original, but all
of which together shall constitute one and the same instrument. 


  

	3.	 This Amendment and the rights and obligations of the parties hereunder shall be governed, construed and
interpreted in accordance with the laws of the State of Delaware, without giving effect to principles of conflicts of law. 


  

	4.	 Except as expressly provided in this Amendment, all terms and provisions of the Agreement shall remain
unmodified and in full force and effect. 


 (Signature Page Follows) 

  
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 IN WITNESS WHEREOF, the parties have executed this Amendment to the Agreement as of the date
first written above 
  

			
	COMPANY:
	
	PROGENITY, INC.
		
	By:	 	 /s/ Harry Stylli

	 Name:
	 	 Harry Stylli

	 Title:
	 	Chief Executive Officer


 (Signature Page to Amendment No. 1 to the Fourth Amended and Restated Investors’ Rights
Agreement) 












 IN WITNESS WHEREOF, the parties have executed this Amendment to the Agreement as of the date
first written above. 
  

	
	INVESTORS:
	
	 /s/ Harry Stylli

	Name: Harry Stylli


 (Signature Page to Amendment No. 1 to the Fourth Amended and Restated Investors’ Rights
Agreement) 












 IN WITNESS WHEREOF, the parties have executed this Amendment to the Agreement as of the date
first written above. 
  

			
	INVESTORS:
	
	 ATHYRIUM OPPORTUNITIES FUND (A) LP

		
	 By:
	 	 Athyrium Opportunities Associates LP,
 its
General Partner

		
	 By:
	 	 Athyrium Opportunities Associates GP LLC,

the General Partner of Athyrium Opportunities Association LP

		
	 By:
	 	 /s/ Andrew C. Hyman

	 Name:
	 	Andrew C. Hyman
	 Title:
	 	Authorized Signatory
	
	ATHYRIUM OPPORTUNITIES FUND (B) LP
		
	 By:
	 	 Athyrium Opportunities Associates LP,
 its
General Partner

		
	 By:
	 	 Athyrium Opportunities Associates GP LLC,

the General Partner of Athyrium Opportunities Associated LP

		
	 By:
	 	 /s/ Andrew C. Hyman

	 Name:
	 	Andrew C. Hyman
	 Title:
	 	Authorized Signatory


 (Signature Page to Amendment No. 1 to the Fourth Amended and Restated Investors’
Rights Agreement) 












 
			
	ATHYRIUM OPPORTUNITIES III ACQUISITION 2 LP
		
	By:	 	 Athyrium Opportunities Associates III LP,
 its
General Partner

		
	By:	 	 Athyrium Opportunities Associates III GP LLC,
the General Partner of Athyrium

Opportunities Associates III LP

		
	By:	 	 /s/ Andrew C. Hyman

	Name:	 	Andrew C. Hyman
	Title:	 	Authorized Signatory


  

			
	ATHYRIUM OPPORTUNITIES III CO-INVEST 1 LP
		
	By:	 	Athyrium Opportunities Associates Co-Invest LLC, its General Partner
		
	By:	 	 /s/ Andrew C. Hyman

	Name:	 	Andrew C. Hyman
	Title:	 	Authorized Signatory


 (Signature Page to Amendment No. 1 to the Fourth Amended and Restated Investors’
Rights Agreement) 












 
			
	ATHYRIUM OPPORTUNITIES 2020 LP
		
	By:	 	 Athyrium Opportunities Associates III LP,
 its
General Partner

		
	By:	 	Athyrium Opportunities Associates III GP LLC,
the General Partner of Athyrium Opportunities Associates III LP
		
	By:	 	/s/ Andrew C. Hyman
	Name:	 	Andrew C. Hyman
	Title:	 	Authorized Signatory


 (Signature Page to Amendment No. 1 to the Fourth Amended and Restated Investors’
Rights Agreement)