NOVATO -- Ultragenyx Pharmaceutical, Inc. (Nasdaq: RARE) on Wednesday closed its initial public offering after netting an estimated $126.4 million, well above what the developer of orphan drugs was initially seeking.

The Novato-based drug maker, one of two spinoffs from San Rafael-based BioMarin Pharmaceutical, initially said it hoped to raise $86.25 million from the sale of 4.8 million shares priced between $14 and $17.

Then last week, Ultragenyx upped the asking price to $21 and expanded the offering to 5.76 million shares and raise $112.5 million before expenses, according to the prospectus filed Friday with the Securities & Exchange Commission. But the stock started trading on the Nasdaq Global Market last Friday at $45.80 a share and was $42 after 3.47 million shares were sold by the end of the session.

At the close of trading today, shares of Ultragenyx were $36.08 each, down 18 cents, or 50 percent, from Tuesday.

The total proceeds from the offering of more than 6.6 million shares of common stock at $21 a share include a deduction of underwriting discounts and commissions. The sold shares include the exercise in full by underwriters to purchase up to 864,054 additional shares of common stock.

J.P. Morgan Securities LLC and Morgan Stanley & Co. LLC are acting as the joint book-running managers for the offering. Cowen and Company, LLC is acting as lead manager, and Canaccord Genuity Inc. is acting as co-manager.

The company had an accumulated deficit of $56.8 million during its development stage as of Sept. 30 and a net loss of $23.8 million for the first nine months of 2013, according to documents. The 59-employee company had roughly $6 million in cash and cash equivalents at that time.

The nearly 5-year-old company is testing the waters of the market that has shown great interest in the life sciences.

The company, founded CEO Emil Kakkis, currently has four drugs in clinical trials. Chief among them are UX-001, its flagship that aims to treat hereditary body myopathy; UX-023, which targets the rare bone disease hypophosphatemia that leads to bowed legs and muscle weakness; and UX003, an enzyme replacement therapy designed for the treatment of mucopolysaccharidosis (MPS) type 7, an extremely rare form of MPS also called Sly syndrome.