The Nazis killed around 160,000-180,000 German Jews, according to the US Holocaust Memorial Museum. That number ignores incidental deaths, caused for example by the destitution of Jews forced out of Germany who died due to causes that might have been alleviated had they not been impoverished when the Nazis seized all of their property. In January 1933, there were roughly 520,000 Jews in Germany, and as you mentioned, many fled in the 6 years before the start of WWII (over half). Almost all of those who remained were killed. While it's unclear how a Jewish German "boy" would fare based on their age group, the deaths of 160,000 Jews would put the rough proportion of the Jewish German population at over 30% of German Jews present in Germany back in 1933. That proportion, of course, would be higher without the fleeing of so many.

German deaths, military and civilian, have a variety of estimates. I've seen them go as high as 9 million, though I doubt that is the best estimate. The better estimates usually range around 7.5 million at most, of a population that in 1933 was 65 million, and grew to 79 million with the addition of new territories acquired by Germany (i.e. Sudetenland). In no scenario is the proportion of deaths close to the number of Jewish Germans killed, even if we take the highest estimates of German casualties against the population in 1933 (only reaches 14%).