Table 1.

Three novel non-synonymous mutations that satisfied the filtering criteria across the 323 variants shared on the X chromosomes between the two half-brothers

Chromosome	bp position (hg19)	Gene	Variant type	Variant info	Phylop+	Polyphen	CADD	Gerp++
X	109507771	AMMECR1	ns	AMMECR1:NM_015365:exon2:c.G530A:p.G177D	0.998909	1	5.776826	5.27
X	53221984	KDM5C	ns	KDM5C:NM_001146702:exon24:c.G4082A:p.R1361K		0.033	1.26541
X	140994109	MAGEC1	ns	MAGEC1:NM_005462:exon4:c.G919A:p.V307M	0.868789	0.512688		0.157

A total of 18 049 variants were shared between the half-siblings. The filtering strategy applied was limited to shared variants on the X chromosome only (323 annotated). 318 variants were removed due to their occurrence within the Southampton control cohort of exomes (n=156) regardless of annotated zygosity. Of the five remaining variants, one was removed due to its synonymous annotation, and another was disregarded due to its low MaxEnt splicing score (<3). Three novel (absent from ExAC server, dbSNP and the Southampton in-house control database) non-synonymous variants satisfied the full filtering criteria. Ns, non-synonymous; sp, splicing.