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Table 2 Overview results of WES in Family A

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

Chr. Genomic DNA Ref. Aberration Reads Variation readsa Gene Messenger RNA Protein PhyloP Confirmedb Segregationc 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 Nod 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 Nod 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 Noe 13.65 Deleterious (score: 0.03) Disease causing (p value: 0.689) Possibly damaging (score: 0.483) 0
  1. aVariation reads: number of variant reads (% of total reads)
  2. bVariant confirmed in proband by Sanger sequencing
  3. cSegregation of confirmed variant with phenotype in respective family
  4. dThe variants in GAS2L3 were both inherited from the (healthy) mother
  5. eThe single confirmed variant in ARID1A was inherited from the (healthy) mother and was not present in the affected brother of the proband