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Jonathan and his teacher, 53-year-old Karen Elaine Smith, were shot by Smith's estranged husband, 53-year-old Cedric Anderson.
Jonathan and another student, 9, were rushed to an area hospital. Jonathan died before making it to surgery, while the 9-year-old was reported to be in stable condition after initially described to be in critical condition.
VIDEO: San Bernardino community holds vigil in wake of shooting
San Bernardino community holds vigil in wake of shooting
Police said the children shot were not targeted and were likely struck by accident.
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The shooting happened in a special needs classroom that included students from grades 1-4. At the time, the room held 15 students, one teacher and two adult aides.
MORE: Children, parents embrace in emotional reunions after San Bernardino shooting
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Jonathan's family set up a GoFundMe account for funeral expenses. To donate, visit https://www.gofundme.com/jonathan-our-family-angel-ngeljonathan.