Disclosure: I'm a founder of a YC company, but am not on YC staff and have no internal knowledge so don't read this as an official YC answer. Reference checks

Disclosure: I'm a founder of a YC company, but am not on YC staff and have no internal knowledge so don't read this as an official YC answer. Reference checks aren't normally part of the selection process, so it's not a normal occurrence for your employer to be contacted, whether or not they're a YC-funded company. I have heard of a case years ago when a founder of a YC company got upset that a newly-appointed employee was applying to YC as a founder of another startup, without revealing he would be doing this when he applied and accepted the job. In this case, YC partners played a role in resolving the dispute, but I don't think it was YC staff who initially alerted the employer. The dispute was more about the perceived dishonesty of the employee in committing to a new role while having a strong intention to leave soon if his own startup was accepted into YC, so it was more about honesty and integrity than merely losing a team member. YC does look for founders with decency and integrity, so it will matter to them that you've been upstanding in how you handle things with your employer. Equally, you are entitled to follow the path that seems best for your long-term interests, and indeed a really good employer will be supportive and encouraging of you pursuing your ambition to become a founder just as they've done themselves. Ideally they should be willing to recommend you to YC and be a mentor for you, but it's more likely to get this kind of support if you're transparent and good-natured in the way you conduct yourself.