• Vital signs was added as an assessment at the home health Week 1 visit for repeat dose (RD) cohorts. • Home health visits were added at Weeks 3, 5, and 7 for RD cohorts that included the following assessments: AEs, concomitant medications, hematology, chemistry, urinalysis, serum C-reactive protein (CRP), nutrition diary, and continuous glucose monitor (CGM). • Sample collection for anti-drug antibody (ADA) analysis was added at Weeks 2 and 6 for RD cohorts • An optional vital sign assessment was added at the time of discharge for all subjects • The SAD cohort data review was updated from an internal review to a review by the independent data monitoring committee (DMC). • The interval between dosing of individual subjects within SAD cohorts was updated from a minimum of 48 hours to a minimum of 72 hours. • Coronavirus 2019 (COVID-19) testing by real time – polymerase chain reaction (RT-PCR) was added to the Initial Screening Visit. • Hemoglobin A1C was added to the Initial Screening Visit for both the SAD and RD cohorts, as well as the Week 12 and Week 48/EOS Visit for the RD cohorts • Criteria for discharge 24 hours after the end of study drug administration were added. • Guidance on communication and seeking immediate medical attention was added. • The following inclusion criterion were added: o Criteria to ensure enrolled subjects have clinically significant disease manifestations that are likely to be improved by UX053 treatment. o “alanine aminotransferase (ALT) ≤ 5x upper limit of normal (ULN) during the 3 months prior to the Baseline Visit.”

(con't) • The following exclusion criteria was added: o “Receipt of only 1 of 2 planned doses of a coronavirus disease 2019 (COVID-19) vaccine. Subjects who have not received a COVID-19 vaccine, and those who have completed COVID-19 vaccination are eligible” and “Symptomatic COVID-19 infection.” Additionally, guidance around the ability and timing to receive the COVID-19 vaccine and measures taken to minimize risk to COVID-19 exposure were added o “Severe renal impairment defined as a defined as a glomerular filtration rate (GFR) ≤ 29 mL/min (Levey et al., 2005).” o “Poorly controlled hypothyroidism, based on the judgement of the Investigator or Ultragenyx, whichever is most conservative” o “History of chronic coagulopathy, thrombophilia, or disorder of complement activation” o “Use of concomitant medications that alter PT/INR, including warfarin and direct oral anticoagulants (eg, rivaroxaban, apixaban, and edoxaban). Patients who receive medications that affect platelet function, such as aspirin or clopidogrel, are allowed unless they have comorbidities that in the judgment of the Investigator place them at undue risk to participate in the study.” o “Current treatment with long-term immunosuppressive medications. This includes subjects with autoimmune conditions managed with immunosuppressive medications and solid organ transplant recipients.” o “Active tuberculosis requiring treatment in the past 3 years.” o “History of active alcohol and/or drug abuse that in the Investigator’s assessment would impair the subject’s ability to comply with the protocol.” o “Females of childbearing potential with hepatocellular adenoma who are unwilling to use nonhormonal contraception.” o Poorly controlled diabetes and its definitions o Resistant hypertension

(con't) • The exclusion criterion “Presence or history of any hypersensitivity reactions to UX053 or its excipients that, in the judgment of the Investigator, places the subject at increased risk for adverse effects” was updated to “Presence or history of any hypersensitivity requiring medical evaluation and management (including injection/infusion associated reactions, such as lymphadenopathy) to UX053, its excipients, or any drug products that contain polysorbate or polyethyleneglycol (PEG). This may include mRNA-based vaccines that contain PEG or polysorbate.” • If dexamethasone (or equivalent) was used as a rescue medication, premedication with dexamethasone (or equivalent) should be considered for all subjects’ subsequent infusions. • Text was added to indicate that Ultragenyx would no longer reserve the right to discontinue subjects or the study for administrative reasons. Subjects only eligible for removal from the study due to withdrawal of consent. • Subject-level Redosing and Stopping Criteria was added, including requirements for redosing study drug, criteria that exclude subjects from redosing (eg, developing new or worsening symptoms of liver disease, receipt of blood products for treatment of consumptive coagulopathy, and specific elevations in ALT levels), and action required in the event that an IRR occurs, as specified by Common Terminology Criteria for Adverse Events (CTCAE) severity. Additionally, text was added to indicate that Ultragenyx would notify the DMC immediately if any subject experienced an event that satisfied subject-level or study-level stopping criteria.

(con't) • The following were added as a study stopping criteria: o Anaphylaxis o “Any TEAE with a severity ≥ Grade 3 (CTCAE version 5.0) affecting the cardiopulmonary, renal, or neurological systems, regardless of relationship to study drug, pending a DMC safety review” o “3 subjects develop platelet counts < 50,000 per mm^3 (or thrombocytopenia ≥ Grade 3 in severity)” o “3 subjects develop international normalized ratio (INR) > 1.5 (or INR increase ≥ Grade 2 in severity)” • The following study stopping criterion was modified from “Increases in serum concentrations of ALT or aspartate aminotransferase (AST) > 2x from Baseline and > 3x theULN, accompanied by increases in serum concentrations of total bilirubin > 2x ULN or INR > 1.5, without any other underlying cause that may account for such changes” to “Increases in ALT or AST > 2x from Baseline and > 3x the ULN, accompanied by total bilirubin > 2x ULN or INR > 1.5, without findings of cholestasis (defined as serum alkaline phosphatase (ALP) activity < 2x ULN) and in the absence of a plausible alternate explanation.” • The following text was added: “Regulatory authorities will be notified immediately if the study stopping criteria are met and study enrollment or dosing is halted.” • Text was added to indicate that subjects will not be replaced if they have received any study drug. • Oxygen saturation was added to the list of vital sign assessments. • R-R was added to the list of measurements calculated for the electrocardiogram assessment. • In addition to glycogen content, muscle fat fraction in the calf was added during the calf 13C Magnetic Resonance Spectroscopy (MRS) assessment. • Text was added to reflect that the AE Cytokine Release Syndrome (CRS) will be graded by the American Society for Transplantation and Cellular Therapy (ASTCT) Consensus Grading for CRS (Lee et al., 2019).

(con't) • The end of the safety reporting period was updated to 28 days following the final dose of study drug or the EOS I (SAD cohorts) and EOS II (RD cohorts) final study visit, whichever occurs later. Additionally, suspected related SAEs could have been reported at any time following the EOS I/II visit. • Magnesium and bicarbonate were added to the list of assessments included in the standard chemistry panel. • The text “plus 90 days for a full sperm cycle” was removed from the following statement: “The time period required is generally determined by the pharmacokinetic properties of the study product and non-clinical reproductive toxicity data, plus 90 days for a full sperm cycle.”

• The following inclusion criterion was removed: o “History of any of the following: a) Severe hypoglycemia, defined as neuroglycopenia (eg, altered mental status, seizure, dizziness, slurred speech, blurry vision, abnormal behavior, perioral paresthesia, requiring intervention by a caregiver) or blood glucose < 54 mg/dL (3 mmol/L) within the last year; b) ≥ 2 incidents of symptomatic hypoglycemia (defined as blood glucose < 70 mg/dL [3.9 mmol/L] if measured at the time of symptoms) within the last year, despite nutrition management c) Ongoing liver injury, defined as alanine aminotransferase (ALT) > 2.5x the ULN within the last year” • The liver MRI, MRS, Fibroscan/ultrasound elastrography, and calf MRS occurring during screening was moved from the Stablization Visit (STV) to the Initial Screening Visit (ISV). • At the discretion of the Investigator, with input from Ultragenyx and the DMC, and based on the emerging safety profile of UX053, additional premedications and rescue medications were allowed to reduce the risk and severity of immune reactions in RD cohorts. Premedication and rescue medication selection were based on the nature of the reactions being observed and the risks of such medications in patients with GSD III. • A row was added to the schedule of events table to indicate the visit windows. • Edits were made to reflect that handheld glucometer (HHG) and CGM data went from being entered by the site in the case report form (CRF) to being uploaded weekly by subjects on a study-provided laptop • Appendix 3 was updated to include all laboratory assessments instead of only safety laboratory assessments. Related to this change, creatine kinase was removed from the chemistry panel in Appendix 3, as it is already collected under Skeletal Muscle & Strength Assessments

(con't) • Text clarified that for the SAD cohorts, a complete physical exam was required at the Screening, Baseline, and End of Study/Early Termination Visits. A targeted physical exam was performed at the Day 1 Visit. • The PROMIS questionnaires, SF-36v2, and GNE Myopathy Functional Activities Scale (GNEM-FAS) were removed from the Screening Visit for SAD cohorts. • Serum B-type natriuretic peptide (BNP) was updated to plasma BNP. • Magnetic resonance spectroscopy (MRS) was no longer limited to 13C MRS.

• Peripheral blood mononuclear cell (PBMC) collection for the assessment of glycogen debranching enzyme (GDE) enzyme activity was removed • RD cohorts were separated into 2 types: double blind (DB)-RD and open label (OL)-RD, as subjects who complete participation in SAD cohorts could be rescreened and enrolled into OL-RD cohorts, receiving 4 additional doses of UX053 Q4W. DB-RD cohorts still receive 5 total doses of UX053 Q2W. Initiation of OL-RD cohorts was designed to run in parallel with initiation of DB-RD cohorts, guided by DMC review. During rescreening for OL-RD cohorts, subjects would have been assessed for status of diet optimization and stability based on nutrition data collected during participation in SAD cohorts and rescreening for OL-RD cohorts. A schematic was added to illustrate nutrition optimization and stabilization requirements during screening. • Reflecting the addition of a Q4W dosing regimen, the secondary endpoint was updated to “PK parameters of AGL mRNA and ATX95, which may include Tmax, Cmax, AUClast, AUCinf, AUCtau (RD cohorts only), accumulation ratio (RAUC; RD cohorts only), Tlast, T1/2, CL, Vss” • One new inclusion criterion and 1 new exclusion criterion were added to allow rescreening of subjects from the SAD cohorts as they enter the OL-RD cohorts (noted above). Existing eligibility criteria that referred to RD cohorts were edited to specify how the criteria apply to the new OL-RD cohorts. The newly added inclusion criterion is: For subjects rescreening into OL-RD cohorts, after treatment with UX053 in a SAD cohort, subjects must meet the following criteria: a) If a significant rise in ALT occurs after the prior dose, ALT should show a decreasing trend toward the subject’s baseline value; b) Total bilirubin is within normal limits; c) Platelets are within normal limits; d) INR is within normal limits.

(con't) The additional exclusion criterion is: For subjects rescreening into OL-RD cohorts, any of the following after treatment with UX053 in a SAD cohort [are excluded]: a) New or worsening symptoms of liver disease (including new or worseninghepatomegaly) along with any increase in transaminase levels; b) Receipt of any blood product administration (eg, packed red blood cells, platelet, fresh frozen plasma) for management of consumptive coagulopathy; c) An ALT level that is ≥ 8x ULN and > 2x the subject’s baseline value in the absence of an alternative explanation. • An optional controlled fasting challenge (CFC) was added for subjects in RD cohorts. • SAD cohorts 3S and 4S were updated to comprise of 2 subjects instead of 3 subjects. • Dose escalation plans were clarified, with an aim to test at least 3 dose levels of UX053. Text was added to indicate that dose levels for each cohort may be altered depending on safety, PK, and pharmacodynamic (PD) findings from prior cohorts, with a maximum dose of 0.30 mg/kg. Cohorts 4S and 4R, in which subjects were to receive single or multiple doses of UX053 at 0.30 mg/kg, respectively, were made optional. • The total number of subjects included in the study was updated to approximately 18, reflecting 6 planned subjects in Cohorts 1S, 2S, and 3S and 12 planned subjects in Cohorts DB-1R, DB-2R, and DB-3R. Text was added to clarify that additional subjects may be added to SAD or RD cohorts for further characterization of safety. • Reference to the Pharmacy Manual regarding guidance on dose reductions was removed. If a subject in a RD cohort (either DB or OL) developed a TEAE/serious TEAE ≥ Grade 3 that was considered by the Investigator to be related to study drug or an intolerable TEAE in a RD cohort, any further study drug administration and any subject-level dose reductions should have been discussed with the Medical Monitor.

(con't) • Text was edited to clarify that telephone calls regarding the use of CGM andHHG devices will occur as needed, outside of scheduled study visits. • Text was added to clarify that subjects within a given RD cohort can be dosed simultaneously. After initiation of repeat dosing, subjects will follow a Q2W (DB-RD cohorts) or Q4W (OL-RD cohorts) dosing regimen. • The italicized text was added to the following inclusion criterion “Willing and able to provide access to medical records surrounding medical treatment that occurred prior to enrollment and during the study.” • The exclusion criterion “Planned surgery, including dental surgeries, during the SAD Period for subjects in Part 1 or prior to Week 10 of the RD Period for subjects in Part 2” was updated to “Planned surgery, including dental surgeries, during the study.” This text was also updated in the section regarding restricted procedures. • For all cohorts, nutrition diary recordings were changed to be recorded at least 3 consecutive days per week through Screening and for the 3 consecutive days in the week leading up to each subsequent visit • Assessments for serum CK – muscle/brain (CK-M/B), troponin I, and CK, and plasma B-type natriuretic peptide (BNP) were added at Weeks 2, 4, 6, and 8 for the DB-RD cohorts. The assessment for plasma BNP was removed from Initial Screening Visit (ISV). • Assessments for urine beta hydroxybutyrate and whole blood for RNA analysis were removed for all cohorts. • The physical exam and weight assessment was removed from Week 12, 24, and 36 for the DB-RD cohorts. • The Day 42 Visit was removed for the SAD cohort. • Assessment of serum ketones was removed at Week 9 for the DB-RD cohorts. Serum ketones was also changed to capillary ketones for DB-RD cohorts. Also for the DB-RD cohorts, ketones are no longer assessed at the Nutrition Optimization Visit (NOV; previously optional per discretion of the Investigator) and Weeks 1, 12, 24, and 36.

(con't) • The schedule of events tables for the RD cohorts reflects that the imaging assessments (liver MRI, MRS, FibroScan or ultrasound elastography) can occur throughout rescreening (OL-RD) or screening (DB-RD). Imaging assessments were also removed for the DB-RD EOS III W48/ET Visit. • PT/INR was changed to be assessed at all scheduled study visits in the Treatment and Follow-up Period for the DB-RD cohorts. • Plasma glucose tetrasaccharide (Glc4) assessment was removed from the study, and assessments for urine Glc4 were added at Weeks 3, 4, 5, 6, 7, and 9 for DB-RD cohorts. • White blood cell (WBC) and red blood cell (RBC) collection was added for future use. • Additional safety language was added noting that epinephrine should be administered if a subject develops an infusion-related reaction (IRR) that meets diagnostic criteria for anaphylaxis. For all other hypersensitivity reactions ≥ Grade 2 in severity suspected to be due to immune activation, dexamethasone should be the initial rescue medication. Additional text was added to account for rescue medications in the event of severe consumptive coagulopathy and profound complement activation. • The terminology regarding the analyses sets, Safety, Per Protocol, and PK, was updated. • Footnote a in the SAD cohort’s schedule of events table was updated to indicate that there must be a minimum of 10 days between any assessments that are measured at both the Screening and the Baseline Visit • When feasible, quantitation of glycogen using nuclear overhauser enhancement (glycoNOE) (Zhou et al., 2020) of the liver, was added to be collected at the time of the liver MRI/MRS. • Text was added to clarify modification of infusion rate, including “If the total infusion time is extended beyond 4 hours, a blood sample should be collected at the new end of infusion (EOI) time. If the new EOI time overlaps with a prespecified time point, sampling should continue at the next scheduled time point”

(con't) • Text was added defining a stable diet as remaining within the nutritional guidelines for adults with GSD III based on expert recommendations. Additionally, text providing examples of how deviating from a stable diet could have been a protocol deviation was removed. • Scoring of the GNEM-FAS was changed from the clinician, who administers the assessment, to Ultragenyx. • Text was added indicating that a future amendment may occur to add an open-label extension after an interim review of safety, PK, and PD data • In exclusion criterion 9, the text “mRNA-based” was removed from the following sentence “This may include mRNA-based vaccines that contain PEG or polysorbate.” • In the following sentence within exclusion criterion 10, “asymptomatic cardiomyopathy” was updated to “mild cardiomyopathy:” “Asymptomatic cardiomyopathy and left ventricular hypertrophy (LVH) are allowed. • A brief study title was added to the title page. The study title was also edited. • The sentence “If dexamethasone (or equivalent) is used as a rescue medication, premedication with dexamethasone (or equivalent) should be considered for all subjects’ subsequent infusions” was updated to “If dexamethasone (or equivalent) is used as a rescue medication, premedication with dexamethasone (or equivalent) should be considered for that subject’s subsequent infusions after discussion with the Medical Monitor.” • Serum myoglobin, serum biotinidase, and calf MRS were removed from the study for all cohorts. • The Week 12, 24, and 36 Visits for DB-RD cohorts were changed to be conducted at home. As a result, Fibroscan or ultrasound elastography will be conducted at Week 10 instead of Week 12; and GNEM-FAS, Patient-reported Outcomes Measurement Information System (PROMIS), and HHD will be assessed at Week 10, and not at Weeks 12, 24, and 36.