Table 1.

Cutoffs used to classify affected genes as T1, T2, or T3 candidate driver genes

1. Phenotype association
		Weak	Medium	Strong
Disease association score (0–5)	pLI > 0.9 RVIS < 10 HI < 10 DDG2P OMIM	> 0	> 0	> 2
Total phenomatch score		> 0	> 4	> 10
Phenomatches (% of HPO terms with phenomatch score > 5)		> 0	> 10%	> 25%
Mode of inheritance			AD/XD/XR+XY	AD/XD/XR+XY
2. Effect of SV on gene
		Weak		Strong
Gene location		Adjacent	Dup	Adjacent	DEL/TRUNC
Support score (0–6)	TAD disrupted V4C disrupted PCHiC disrupted DHS disrupted RNA expression	> 1	NA	> 3	NA
3. Driver classification
Classification		T3	T2		T1
Phenotype association + effect of SV on gene		Weak + weak	Strong + weak	Medium + strong	Strong + strong

pLI probability of being loss-of-function intolerant, RVIS Residual Variation Intolerance Score, HI haploinsufficiency, DDG2P Developmental Disorders Genotype-Phenotype Database, OMIM Online Mendelian Inheritance in Man, AD autosomal dominant, XD X-linked dominant, XR X-linked recessive, XY male, TAD topologically associating domain, V4C virtual 4C, PCHiC promoter capture Hi-C, DHS DNase hypersensitivity site