Based on his brother's G2G, his LNAB is Wittelsbach. His CLN was von der Pfalz, which was not translated to English (of the Palatinate), his OLN is his house name Pfalz-Simmern (which was a cadet branch of the house of Wittelsbach).
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It may be possible to confirm family relationships with Rupert by comparing test results with other carriers of his Y-chromosome or his mother's mitochondrial DNA.
However, there are no known yDNA test-takers in his direct paternal line.
Mitochondrial DNA test-takers in the direct maternal line: