B3GALNT2 mutations associated with non-syndromic autosomal recessive intellectual disability reveal a lack of genotype–phenotype associations in the muscular dystrophy-dystroglycanopathies

Table 2 Overview results of WES in Family A

Chr.	Genomic DNA	Ref.	Aberration	Reads	Variation reads^a	Gene	Messenger RNA	Protein	PhyloP	Confirmed^b	Segregation^c	CADD	SIFT	MutationTaster	Polyphen2	Allele frequency in gnomAD
Compound heterozygous variants
1	235628968		Dup AA	273	57 (21%)	B3GALNT2	c.822_823dup	p.Ile276Leufs*26	3.624	Yes	Yes	-	-	-	-	0.0002057
1	235621948	G	A	100	30 (30%)	B3GALNT2	c.988C > T	p.Arg330Cys	1.708	Yes	Yes	29.3	Deleterious (score: 0)	Disease causing (p value: 1)	Probably damaging (score: 1.000)	0.00001234
12	101016068	G	A	.	37 (36%)	GAS2L3	c.664G > A	p.Glu222Lys	5.61	Yes	No^d	27.6	Deleterious (score: 0.03)	Disease causing (p value: 1)	Possibly damaging (score: 0.563)	0.001949
12	101016071	G	A	.	38 (37%)	GAS2L3	c.667G > A	p.Asp223Asn	5.61	Yes	No^d	24.8	Deleterious (score: 0.02)	Disease causing (p value: 1)	Benign (score: 0.392)	0.001956
Variants in known intellectual disability genes
1	27105725	A	G	.	10 (45%)	ARID1A	c.5336A > G	p.Glu1779Gly	0.69	Yes	No^e	13.65	Deleterious (score: 0.03)	Disease causing (p value: 0.689)	Possibly damaging (score: 0.483)	0

^aVariation reads: number of variant reads (% of total reads)
^bVariant confirmed in proband by Sanger sequencing
^cSegregation of confirmed variant with phenotype in respective family
^dThe variants in GAS2L3 were both inherited from the (healthy) mother
^eThe single confirmed variant in ARID1A was inherited from the (healthy) mother and was not present in the affected brother of the proband

ISSN: 1756-994X