BioMarin/Whistlestop/EDEN Housing

999 Third Street

Address:999 Third Street
Project Numbers:ZC18-002, ZO18-003, S18-001, ED18-087,
UP18-034, GPA18-001, DA18-001, SP18-006

CDR17-008-- completed 03/14/2018
Applicant:BioMarin, Shar Zamanpour
Project Planner:Sean Kennings
(415) 533-2111
Biomarin E and P
Whistlestop E and P

Project Description

BioMarin, in conjunction with Whistlestop/Eden Housing, submitted a planning application for a proposed development on 999 3rd Street in downtown San Rafael. The project site, between 2nd and 3rd Streets (at the corner of Lindaro), is approximately 133,000 square feet in size. The property owner, BioMarin, proposes to construct two, four-story 69’ tall buildings for the purposes of laboratory/R&D and general office spaces. A third building, a six-story senior center / senor housing development, would be constructed by Whistlestop/Eden Housing on a 15,000 sq ft portion of the property at the corner of Brooks and 3rd Street. BioMarin’s buildings would each be four stories but with large floor to ceiling heights to accommodate infrastructure and facilities for their laboratory/research & development needs. The proposed components of the project are not covered by the 1998 San Rafael Corporate Center (SRCC) master plan approvals (per PD 1936).

The formal application requires review and approval by the Design Review Board and the Planning Commission and ultimate approval by the City Council for in order to proceed.

The application includes the following:

  • Expansion of the existing Planned Development (PD) zoning designation that applies to the SRCC to encompass the 999 3rd Street property.
  • General Plan Amendments to: 1) modify the maximum intensity of nonresidential development and assigned floor area ratios (FARs), reducing the FAR of the 999 3rd Street site from 1.5 to 0.9 and increasing the FAR of the SRCC to 0.9, with 0.9 as a blended ratio across the expanded PD; 2) allow for the use of blended FAR for Downtown PDs under single ownership or unified control, consistent with current General Plan Policy LU-9.b.2 which allows for a transfer of FAR among Downtown project sites; and 3) establish a height bonus for the 999 3rd Street site in exchange for BioMarin providing specified amenities and community benefits.
  • The BioMarin portion of the project is requesting a 16’ to 20’ height bonus as a requirement to facilitate the four-story laboratory floorplates of 17’. Per the SRMC Section 14.160.190 (A)(3) the project would be allowed a maximum height bonus of 12’ contingent on providing affordable housing, public parking, or skywalks over 2nd/3rd street. In 1998, the SRCC campus plan was approved with a height bonus of 24’ (54’ to 78’) based on concessions as required by the San Rafael Municipal Code Section 14.160.190(A)(2) for development in the Lindaro Office district.
  • Approval of a height exception as allowed through three potential methods:
    • Expansion of the existing SRCC PD to include 999 3rd Street, and therefore application of the PD’s height bonus to 999 3rd Street in exchange for the provision of public benefits (as discussed in the preceding bullet);
    • Height exception for special use buildings pursuant to Section 14.24.020 of the Zoning Ordinance (discussed below); and
    • Height bonus provided in exchange for public benefits in the 2/3 MOU pursuant to Section 14.16.190 of the Zoning Ordinance (discussed below).
  • Approval of parking ratios appropriate to the proposed uses, considering the overall needs of the SRCC and the effectiveness of BioMarin’s Transportation Demand Management (TDM) Program, which would be expanded to apply to the entire BioMarin campus in San Rafael, including the 999 3rd Street site. BioMarin’s application also includes a contingency plan that addresses future scenarios in case of a change in tenancy or ownership that results in a greater parking demand than assumed for this project.

BioMarin’s proposal also provides the following public benefits:

  • Donation of a portion of the property, valued at $1.2 million, for the development of a healthy aging center and affordable senior housing;
  • 3,500 square feet of retail space and 6,000 square feet of landscaped plaza open to the public during daytime hours at the corner of 3rd and Lindaro streets;
  • Donation of funds for the development of a bike lane on Lindaro Street from 3rd Street to Anderson Drive; and
  • Donation of funds to enhance pedestrian safety with improved sidewalks and crosswalk design at the corner of Lindaro and 2nd streets, as well as 3rd Street and Lootens Place.

Whistlestop’s portion of the project also proposes the following concessions:

  • Approval of a mixed-use building for Whistlestop/Eden Housing with additional residential density and height, and reduced landscaping and parking via application of the State’s Density Bonus Law and in accordance with Section 14.16.190 of the City’s Zoning Ordinance.

The Whistlestop portion of the project would include a requested 16-ft height bonus as a concession under the State Density Bonus law and under the City’s density bonus provisions and is considered a minor concession. Minor concessions are granted if a project provides the required affordability and the concession does not require the submittal of a financial pro forma by the applicant. The project’s planning entitlements would typically require Planning Commission review and approval, based on the recommendations of the Design Review Board (Board).

  • Density bonus to allow up to 74 units;
  • Landscaping reduction from 10% to 3%
  • Parking reduction for senior living resident

Current Status

The project was reviewed as a Conceptual Design Review by the Design Review Board on February 6, 2018 and then by the Planning Commission on February 27, 2018.

The project was then reviewed by the Planning Commission on May 14, 2019 as a study session and then by the Design Review Board as a formal application on June 18, 2019. The DRB will hold a follow-up review on the recommendations made during their June 18th meeting on August 20, 2019.

Concurrently, the City of San Rafael has contracted with Amy Skewes-Cox to prepare an Environmental Impact Report (EIR) pursuant to the California Environmental Quality Act (CEQA). The EIR evaluated potential project impacts for areas of environmental concern such as, visual impacts, traffic and circulation, air quality, noise, greenhouse gas emissions, hydrology and drainage, and hazardous materials. A scoping meeting to receive agency and public input regarding the EIR was conducted on March 12, 2019.

The Draft EIR was completed and published for a 45-day public review period, commencing on Friday, August 9, 2019 and ending on Monday September 23, 2019 at 5pm. The public review period concluded with a public hearing before the Planning Commission on Tuesday, September 24, 2019. The Commission accepted all written and oral comments and directed staff to prepare the Final EIR.

The Final EIR has been completed and released for public review on January 13, 2020 The Planning Commission will conduct a public hearing on Tuesday, January 28, 2020 to consider the Final EIR, along with the project merits and planning applications and provide their recommendation to the City Council..

Written comments should be sent to City of San Rafael, Community Development Department, 1400 Fifth Ave, San Rafael, California 95901; Attn: Sean Kennings, Contract Planner. Comments may also be sent by email to with the heading “BioMarin/ Whistlestop/ Eden Housing Project” in the subject line.

Past Meeting Information

Meeting Type
February 6, 2018 (Conceptual Design Review)Design Review BoardStaff Report
February 27, 2018 (Conceptual Design Review)Planning CommissionStaff Report
March 12, 2019 (EIR Scoping/Notice of Preparation)Planning CommissionStaff Report
May 14, 2019 (Study Session)Planning CommissionStaff Report
June 18, 2019 (Formal Design Review)Design Review BoardStaff Report
August 20, 2019 (Final Design Review)Design Review BoardStaff Report
September 24, 2019 (Draft EIR hearing)Planning CommissionStaff Report
January 28, 2020 (Final EIR and project merits)Planning CommissionStaff report **

**Staff report will be posted by the Friday before the meeting date

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