The authors describe results from a detailed sequencing analysis of 5 candidate CL/P genes in a total of 1141 samples. This type of deep analysis is necessary as a follow up to GWAS or WES identified candidates. The results identify variants in all 5 genes, and thus suggest involvement in CL/P. Of course, additional future studies are needed to functionally validate these variants. The manuscript can benefit from some additional detail and some organizational changes. Most importantly, a clear rationale supported with references is required for the 5 genes selected for this analysis.
Concerns:
1. Please mention the number of samples analyzed (1141) in the abstract.
2. Please provide a breakdown of the samples by ethnicity (or country) and phenotype (CLP, CPO, etc) in the methods.
3. Page 5, lines 46-55: Please provide a rationale for why these 5 genes were selected in the introduction.
4. Page 5, lines 46-55: Please provide the references to the GWAS or WES studies that identified these 5 genes as associated with CL/P.
5. Page 9, line 10: please continue to use “variant” throughout the manuscript, instead of “mutation”.
6. Page 9, line 5 vs. lines 10-21: initially it is stated that there are 7 variants in Shh, but in the latter section only 6 are described. Please clarify.
7. Figure 1 is unnecessary – please remove.
8. Figure 2: resolution is low if the expression numbers are meant to be read and compared.
9. Figure 2: why is MRPL53 not included in Figure 2.
10. Figure 3 (page 23): The figure legend is missing. What are the values provided? Especially, compared to the values in Figure 2 – expression or enrichment? Why is Shh not included in this figure. Is the idea is just to provide some expression data for MRPL53? If possible, remove figure 3 and merge the expression information into Figure 2.
11. Page 10, line 34: Please see #4 above and provide references for the GWAS and WES.
12. Page 12, line 31: please provide a reference for the eQTL study
13. Page 14, line 34: please replace “confirm” with “strongly suggest” or “predict” or similar.
14. Discussion: Please remove the HOPE analysis from the discussion and place it into the results section. Preferably, add a Table for the HOPE results if possible for an easy comparison of variants.

Thank you for addressing all of my concerns, except one:
There is still no legend for Figure 2 – I also downloaded the individual files from the OD website, and didn’t see it. Perhaps, it is due to an error in the automated compilation. Either way, a figure legend is necessary since the Author Response points to the legend to answer my original concerns below:

1. Figure 3 (page 23): The figure legend is missing.
   Response: It is there.
   What are the values provided? Especially, compared to the values in Figure 2 – expression or enrichment?
   Response: These are enrichment values and included in the legend.

In addition, the data in Figure 2 are not explained in the methods. The methods appear to describe the enrichment data from SysFACE in Figure 1. However, Figure 2 appears to show simply RNAseq data (not enriched), because the numbers for genes common to Figures 1 and 2 do not match for the palate otherwise. Also, please reference the source of the RNAseq data for Figure 2, i.e. anterior and posterior palate, as these datasets don’t appear in SysFACE.

No concerns.