Table 1.

Genes affected by the complex rearrangements

Gene	Number of BPJs	Chr	Start	End	Transcriptional strand	MIM phenotype	pLI
t(7;11)
ABCA13	2	7	48211057	48687091	+		8.8e−114
ANO3	2	11	26210670	26684836	+	610110	1.2e−17
DCDC5	2	11	30885150	31014233	−		4.7e−8
LOC101927668	2	7	19958604	20180049	−		N.a.
t(X;21;19;4)
ARHGAP24	14	4	86396284	86923823	+		3.9e−10
ABCG2	12	4	89011416	89152474	−	614490, 138900	2.1e−32
AFF1	12	4	87856154	88062206	+		0.71
FAM13A	8	4	89647105	89978346	−		1.9e−18
PRKG2	8	4	82008524	82136271	−		0.65
C4orf22	6	4	81256874	81884910	+		2.1e−9
CYYR1-AS1	6	21	27765954	27941571	+		N.a.
HERC3	6	4	89513574	89629693	+		0.07
MMRN1	6	4	90816052	90875780	+		2.1e−25
NCAM2	6	21	22370633	22914517	+		0.23
NUDT9	6	4	88343728	88380606	+		9.2e−6
CCSER1	4	4	91048684	92523370	+		0.000789
HSD17B11	4	4	88257674	88312455	−		2.1e−7
LOC101928978	4	4	84889235	85220322	−		N.a.
PTPN13	4	4	87515468	87736329	+		1.4e−25
RASGEF1B	4	4	82347547	82393082	−		0.92
MAPK10	3	4	86933449	87374283	−		0.28
CYYR1	2	21	27838528	27945723	−		0.0004
DPY19L3	2	19	32896655	32976799	+		2.9e−7
GPRIN3	2	4	90165429	90229161	−		4.1e−13
HERC6	2	4	89299891	89364249	+		1.5e−14
LINC00989	2	4	80413747	80497614	+		N.a.
LOC100420587	2	19	28926295	29218601	−		N.a.
LOC101928942	2	4	82086094	82114549	+		N.a.
MIR548XHG	2	21	19933583	20132130	−		N.a.
PRR27	2	4	71019904	71032326	+		0.0002

Protein-coding genes in bold

BPJ breakpoint junction, N.a. not applicable