The chromosome positions were not part of Table 1, and had to be extracted manually from Table S2 and S3

cDNA change was back-converted to genomic coordinates using TransVar.

Two PTEN mutations (404dupG and dupC) 

The following mutation was excluded for not having a valid possible transcript: MEF2C:c.403–1G>T

The following mutations were modified to keep only the Dup and left to be handled by Transvar as the reference was not valid:
	PTEN:c.404dupG
	PTEN:c.460dupC
	SHANK3:c.3679dupG
	SHANK3:c.3679dupG


For multiple transcript matches, we selected the transcript that matched the protein mutation.

input	transcript	gene	strand	coordinates(gDNA/cDNA/protein)
IQSEC2:c.1229delC	NM_001111125 (protein_coding)	IQSEC2	-	chrX:g.53283885delG/c.1229delC/p.P410Lfs*59
MEF2C:c.766C>T	NM_002397 (protein_coding)	MEF2C	-	chr5:g.88027590G>A/c.766C>T/p.R256*
MBD5:c.973C>T	NM_018328 (protein_coding)	MBD5	+	chr2:g.149226485C>T/c.973C>T/p.R325*
PTEN:c.404dup	NM_000314 (protein_coding)	PTEN	+	chr10:g.89692920dupT/c.404_404dup/p.C136Mfs*44
PTEN:c.460dup	NM_000314 (protein_coding)	PTEN	+	chr10:g.89692977dupT/c.460_460dup/p.Y155Lfs*25
CDKL5:c.2854C>T	NM_003159 (protein_coding)	CDKL5	+	chrX:g.18668586C>T/c.2854C>T/p.R952*
HEPACAM:c.803+1G>A	NM_152722 (protein_coding)	HEPACAM	-	chr11:g.124793235C>T/c.803+1G>A/.
NF1:c.1742dupT	NM_001128147 (protein_coding)	NF1	+	chr17:g.29548968dupT/c.1742_1742dupT/p.L581Ffs*6
NF1:c.1742dupT	NM_001128147 (protein_coding)	NF1	+	chr17:g.29548968dupT/c.1742_1742dupT/p.L581Ffs*6
NF1:c.1742dupT	NM_001128147 (protein_coding)	NF1	+	chr17:g.29548968dupT/c.1742_1742dupT/p.L581Ffs*6
RNF135:c.1015delG	NM_032322 (protein_coding)	RNF135	+	chr17:g.29325925delG/c.1015delG/p.V339Sfs*42
RNF135:c.1015delG	NM_032322 (protein_coding)	RNF135	+	chr17:g.29325925delG/c.1015delG/p.V339Sfs*42
SHANK3:c.3424_3425del	NM_033517 (protein_coding)	SHANK3	+	chr22:g.51159722_51159723delGG/c.3424_3425delGG/p.G1142Sfs*578
SHANK3:c.3679dup	NM_033517 (protein_coding)	SHANK3	+	chr22:g.51159977dupC/c.3679_3679dup/p.R1227Pfs*494
SHANK3:c.3679dup	NM_033517 (protein_coding)	SHANK3	+	chr22:g.51159977dupC/c.3679_3679dup/p.R1227Pfs*494
TSC2:c.4753_4763del	NM_000548 (protein_coding)	TSC2	+	chr16:g.2136284_2136294del11/c.4753_4763del11/p.K1585Afs*14
MAP2K1:c.199G>A	NM_002755 (protein_coding)	MAP2K1	+	chr15:g.66727483G>A/c.199G>A/p.D67N
TSC2:c.1081C>G	NM_000548 (protein_coding)	TSC2	+	chr16:g.2110776C>G/c.1081C>G/p.L361V