Table 2 Transcription factors significantly enriched for predicted deleterious de novo variants

Gene	LOEUF	de novo variants			Inherited variants		de novo and case/control q value	de novo only q value
Gene	LOEUF	pLoF	MisA	MisB	Case pLoF	Control pLoF	de novo and case/control q value	de novo only q value
Congenital heart defect
GATA6	0.174	3	2	0	0	0	2.5 × 10⁻⁵	3.5 × 10⁻⁶
KMT2A	0.065	5	0	1	0	0	3.2 × 10⁻⁴	5.0 × 10⁻⁵
ADNP	0.123	4	0	0	0	1	5.8 × 10⁻⁴	3.1 × 10⁻⁴
KDM5B^a	0.572	4	0	0	2	4	0.012159	5.2 × 10⁻⁴
NR2F2	0.217	2	1	0	0	0	0.014122	0.002103
FOXP1^a	0.175	2	1	0	0	0	0.029404	0.003100
TBX5	0.135	1	1	0	1	0	0.031389	0.053298
GATA4	0.527	2	0	0	2	1	0.040077	0.050796
TCF12	0.372	1	1	0	2	1	0.051542	0.068473
ZEB2	0.107	1	1	0	1	0	0.058741	0.131609
KLF2^a	0.710	1	1	0	0	0	0.204573	0.032261
SMAD4	0.222	0	2	0	0	0	0.209108	0.035057
MEIS2^a	0.184	2	0	0	0	0	0.271015	0.055872
CTCF^a	0.148	0	2	0	0	0	0.278293	0.058374
Orofacial cleft
SATB2	0.091	7	5	0	0	0	3.86 × 10⁻¹⁴	5.77 × 10⁻¹⁵
TFAP2A	0.261	2	3	0	1	0	2.84 × 10⁻⁶	7.70 × 10⁻⁶
CTCF	0.148	0	3	0	0	0	0.011737	0.001484
IRF6	0.132	1	0	3	1	0	0.002951	0.007637
TP63	0.267	1	1	0	3	0	0.003631	0.072430
SOX5^b	0.188	1	1	0	1	0	0.018728	0.058691
ADNP^b	0.123	2	0	0	0	1	0.092444	0.088307
GRHL2^b	0.270	2	0	0	0	0	0.328840	0.076571

LOEUF loss-of-function observed/expected upper bound fraction³⁶, pLoF predicted loss-of-function, MisA PrimateAI > 0.9, MisB PrimateAI 0.75-0.9.
Q values less than 0.1 are bolded.
^aNovel candidate CHD genes.
^bNovel candidate OFC genes.

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