Table 4

Candidate genes identified through gene disruption or TAD disruption

Gene	OMIM	Putative function	pLI	Patients	Phenotype summary	Gene classification
MAGI	602 625	Guanylate kinase, cellular interaction	1.00	IL/1901	ID, speech delay, cleft palate	VUS
FAM19A1	617 495	Cerebral chemokine	0.86	IL/1901	ID, speech delay, cleft palate	VUS
PPARGC1A	605 417	Energy metabolism regulation	1.00	VJ/0601	ID, speech delay, ASD, FD	VUS
RBM27	–	Unknown	1.00	EB/0401	ID, growth retardation, microcephaly, epilepsy	VUS
TENM2	610 119	Unknown	1.00	EB/0401	ID, growth retardation, microcephaly, epilepsy	VUS
CNTN4	607 280	Contactin, CNS development	1.00	TS/1101	ID, behavioural troubles, FD	VUS
CELF2	602 538	RNA splicing	1.00	TS/1101	ID, behavioural troubles, FD	VUS
CAMK1D	607 957	Serine-threonine kinase	0.99	TS/1101	ID, behavioural troubles, FD	VUS
DCAF5	603 812	Mitochondrial protein	1.00	AG/1003	FD, clubfeet, Crohn’s disease	VUS
UNC79	616 884	Sodium channel subunit	1.00	EC/2302	ID, psychiatric troubles, FD	VUS
RBM26	-	Unknown	1.00	BM/1603	ID, FD CHD,	VUS
SEMA6A	605 885	CNS development	1.00	BM/1201	ID, growth retardation, speech delay	VUS
PKN2	602 549	Unknown	1.00	MD/2203	ID, absent speech, ASD, epilepsy, FD	VUS
STXBP5L	609 381	Exocytosis inhibition	1.00	CM/0103	ID, epilepsy	VUS
DDX24	606 181	RNA helicase	0.22	OP/0701; EC/2302	ID, behavioural troubles	VUS
MDGA2	611 128	Synaptic regulation	0.99	OL/2202; KT/1403	ID, absent/delayed speech	VUS

ASD, autistic spectrum disorder; CHD, congenital heart defect; CNS, central nervous system; FD, facial dysmorphism; ID, intellectual disability; pLI, probability of loss of function intolerance; TAD, topologically associated domain; VUS, variants of unknown significance.