Mutation analysis of FANCD2, BRIP1/BACH1, LMO4 and SFN in familial breast cancer

Breast Cancer Research

Table 3 In silico analysis of novel synonymous and 3' UTR alterations in FANCD2, BRIP1/BACH1 and STN

Gene	Sequence variant	Location	Conserved in mouse^a	Predicted effect on mRNA structure^b	Predicted effect on consensus splice sites^c	Predicted effect on exonic splice site^d
FANCD2	633C>T	Exon 9	Yes	None	None	No change
	2148C>G	Exon 23	No	None	None	Gains SRp55, changes SF2/ASF
	3558C>G	Exon 35	No	Slight shortening of side branch	Loss of exon 35 donor^e	Gains SC35, loses SF2/ASF
BRIP1/ BACH1	430 G>A	Exon 5	Yes	None	None	Loses SRp55 and SRp40, gains SF2/ASF
	584T>C	Exon 6	No	Completely changes mRNA structure	None	Loses SRp40
	3401 delC	Exon 20	Yes	None	None	No change
	3464 G>A	Exon 20	No	Loss of one cluster of stem loops, gain of another	None	Loses SRp40 and SF2/ASF
	3782T>C	3' UTR	No	Additional stem loop in middle of structure
SFN	748G>C	3' UTR	No	Change in branch position
	765C>T	3' UTR	Yes	Change in branch position
	766C>A	3' UTR	Yes	Loss of major side branch
	767C>T	3' UTR	Yes	No change
	775C>A	3' UTR	Yes	No change
	776C>T	3' UTR	Yes	No change
	777C>T	3' UTR	Yes	No change
	786C>A	3' UTR	Yes	Change in branch position
	787C>A	3' UTR	Yes	No change
	792C>T	3' UTR	Yes	No change

^aAccording to UCSC Genome Bioinfomatics [36]. ^bAccording to mFOLD [39].
^cAccording to SpliceSiteFinder [41] and BDGP Splice Site Prediction [37].
^dAccording to ESE Finder [38]. ^eAccording to BDGP Splice Site Prediction [37], but not SpliceSiteFinder [41]. UTR, untranslated region.

ISSN: 1465-542X