Failed Preclinical Course

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Earlier this year I slept in and missed an exam for my Clinical Skills Lab (CSL) course. I don't think I'm going to pass and will probably have to remediate it. I've really wanted a shot in this field, dedicating my past summer towards research. Will CSL be the red flag that kills me? Everyone gets an A in this class so I'll probably be at the bottom of the class rank now. I go to a low tier MD school with no home program.

I might not be thinking very clearly right now, the reality just hit me all at once. Sorry if this is disorganized. I've been told all summer by people how hard it is to match and I'm afraid my app will be immediately thrown out. Assuming the rest of my app is on par with the rest of the pool, do I have a prayer? Or should I start exploring other interests. Thanks for reading, I hope this was not an inappropriate post to make.

Edit: I'm an M2.

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I don't think programs look at the first two years that closely because schools are so heterogeneous in how they do things (many schools are P/F for example) so I agree that third year + Step 1 are the main factors that will end up mattering.
 
An F anywhere in the transcript will potentially be a red flag and an easy selection criteria for programs. This can be ameliorated by strengthening other parts of the application, but most importantly addressing it in the Dean's letter or personal statement since a lack of explanation will have PDs wondering.
 
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