Table 1.

Top 10 genes prioritized by RUNNER in Hirschsprung disease dataset

Gene symbol	Minor alleles	Missense alleles	LOF alleles	Region length	mu_mis	mu_lof	oe_mis	oe_lof	ExonGC	Residual1	P 1	Residual	P
RET	61	56	5	3.477	44.853	2.678	0.896	0.039	0.585	5.265	7.01E-08	5.228	8.58E-08
NXPE4	21	19	2	1.660	13.620	0.996	1.018	1.109	0.415	3.311	4.65E-04	4.649	1.67E-06
CDCA4	19	19	0	0.731	10.045	0.354	0.934	0.452	0.531	3.586	1.68E-04	4.102	2.05E-05
EDNRB	15	13	1	1.797	14.472	1.186	0.806	0.329	0.410	2.840	2.26E-03	4.066	2.39E-05
OGG1	26	20	6	1.732	13.857	1.345	1.103	0.885	0.576	3.498	2.35E-04	4.055	2.50E-05
PHYKPL	22	20	1	1.452	16.346	0.929	1.081	0.961	0.562	3.096	9.81E-04	3.921	4.42E-05
GAB4	33	32	1	2.105	18.445	0.889	1.149	0.815	0.578	3.820	6.66E-05	3.766	8.29E-05
MOGAT2	15	15	0	1.035	13.006	0.852	1.047	0.378	0.546	2.547	5.44E-03	3.481	2.50E-04
KIAA1257	31	26	5	3.452	12.522	0.811	0.896	0.871	0.481	3.823	6.58E-05	3.433	2.99E-04
BECN1	15	15	0	1.408	13.371	1.384	0.666	0.151	0.481	3.240	5.99E-04	3.397	3.40E-04

Notes: Minor alleles refer to rare nonsynonymous minor alleles in the tested cases. The minor allele counts to missense is summed in Missense alleles, and the minor allele counts to loss-of-function (stopgain, splicing, frameshift) is summed in LOF alleles. Region Length and ExonGC are the length (kb) and GC content in exon regions of the gene. mu_mis and mu_lof refer to the gene's mutation rate based on missense variants and loss-of-function variants in its canonical transcript, respectively. oe_mis and oe_lof refer to the gene's observed over expected ratio at missense and loss-of-function variants obtained from gnomAD, respectively. Residual₁ and P₁ denote the deviance residual and P-value generated by RUNNER1 (the equal-weight (weight = 1) version of RUNNER). Residual and P mean deviance residual and P-value generated by RUNNER.