Novel Synonymous and Deep Intronic Variants Causing Primary and Secondary Pyruvate Dehydrogenase Complex Deficiency

Table 2

Sequence and in silico prediction scores for splice sites created by the variants and the activated splice sites.

Position		Sequence	SSF (0-100)	MaxEnt (0-16)	NNSPLICE (0-1)	GeneSplicer (0-21)	SpliceAI (0-1)
PDHX c.1023+2267A>G	WT	AAG/ATAATAGATT	0	0	0	0	NA
	Variant (DS)	AAG/GTAATAGATT	81,97	8,49	0,93	3,72	Δ0,99
PDHX c.1023+2302A>G	WT	CCC/ATAAGTCTTC	0	0	0	0	NA
	Variant (DS)	CCC/GTAAGTCTTC	77,77	9,09	0,98	0	Δ0,94
PDHX c.1023+2191	Activated AS	TTTTGAGCAG/CAG	0	5,91	0	0,8	NA
TPK1 c.185+15054G>A	WT	TCTTTCTTGG/GTA	0	0	0	0	NA
	Variant (AS)	TCTTTCTTAG/GTA	88,46	12,03	1,0	12,65	Δ0,99
TPK1 c.185+15183	Activated DS	GAG/GTGAAGACCA	75,41	4,41	0	1,38	NA

Abbreviations: AS = acceptor site; DS = donor site; NA = not applicable; SSF = SpliceSiteFinder-like; WT = wild type. The nucleotides changed by the variants are underlined. Reference sequences: RefSeq NM_003477.3 for PDHX and NM_022445.3 for TPK1.