pCADD: SNV prioritisation in Sus scrofa

Table 2 Seven well-known examples of causal SNVs with different effects on phenotype and their pCADD scores

Genomic location	Ref	Alt	pCADD	Percentile	Gene	Effect	Citations
6:146829589	G	A	22.868	99.5	LEPR	Missense: affects productive, fatness and meat quality traits in different genetic backgrounds	[44]
1:265347265	A	G	17.198	98.1	NR6A1	Missense: affects number vertebrae	[45]
17:57932233	A	C	23.322	99.5	PCK1	missense: causal mutation associated to intramuscular fat content, backfat thickness and meat quality in pigs	[46]
7:31281804	G	A	21.589	99.3	PPARD	Missense: affects ear size, fat metabolism, skin and cartilage development	[47]
12:38922102	G	A	21.848	99.3	TADA2A	Splice-donor: lethal recessives	[48]
3:43952776	T	G	10.144	90.3	POLR1B	Splice-region: lethal recessives	[48]
6:54880241	T	C	28.767	99.9	PNKP	Missense: lethal recessives	[48]

Both the pCADD scores and percentiles indicate their rank as candidate causal SNVs among all potential SNVs in the pig genome

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