Novel BCAP31 alternative splicing transcripts in patient
The novel variant
(NM_001256447.2:c.92G>A)
sits at the 2nd anticodon that encodes the
31th amino acid of BCAP31 which is highly conserved in
vertebrates. Moreover, the variant is part of a consensus 5’ donor
splice site sequence at the end of the exon. We evaluated the wildtype
and variant allele sequence by the Human Splicing Finder (HSF) (Desmet
et al., 2009) to see whether the variant would cause any changes to the
splice site. The HSF predicts that the wild type G allele position is a
donor splice recognition site (underlined G in
CTCCTAAAAG gtatggccta), but that the mutant A allele will alter
the donor site recognition, thereby disrupting proper splicing.
To confirm the hypothesis that the A variant in the patient’sBCAP31 gene would lead to improper splicing, we examined the
transcript pattern of white blood cells (WBCs) in the patient and her
parents by RT-PCR followed by Sanger sequencing (Fig 3). The results
showed that there were no wildtype transcript in the patient’s WBCs, but
that two novel transcripts were found. The major novel transcript is
devoid of exon 2
(NM_001256447.2:r.54_190del,
p.Ser2AlafsTer42) while the minor
transcript has a 110nt insertion in intron 2
(NM_001256447.2:r.190_191ins[g>a;190+1_190+110],
p.Arg31LysfsTer11). The major transcript leads to a frameshift
transcript utilizing a new start codon site in exon 3.
In summary, a de novo heterozygous variant in the patient results
in a novel frameshift transcript that replaces the wildtype form of
BCAP31. This variant is deemed Pathogenic (ACMG criteria PS2, PS3, PM2,
PP3, PP4), according to de novo variant (PS2), RT-PCR study
(PS3), absent from controls (PM2), deleterious effect on the gene
product (PP3), and clinical phenotype (PP4) based on the criteria of
ACMG/AMP 2015 guideline (Li & Wang, 2017).