Table 2.

In silico predictions and reported frequencies of detected CACNA1H variants.

	W1530S	G1064R	A1989Rfs*33	I1430T	L1447M	E1259Gfs*85
Cohort	Karolinska	Karolinska	Karolinska	TCGA	TCGA	TCGA
Case no.	6	19	E2	WB-A81D	QR-A70U	S7-A7WP
DNA alteration	c.4589G>C	c.3190G>A	c.5965_5987del	c.4289T>C	c.4339T>A	c.3776del
Conserved amino acid	Highly	Highly	–	Highly	Highly	–
In silico predictions
Mutation Taster (v2021)	Deleterious	Deleterious	Deleterious	Deleterious	Benign	Deleterious
Tree vote (del/benign)	75/25	69/31	–	86/14	27/73	–
PolyPhen2	Probably damaging	Probably damaging	–	Probably damaging	Probably damaging	–
Score	0.998	1.000	–	0.998	0.999	–
CADD (v1.6) phred score	29.4	28.9	–	25.1	21.8	–
SIFT (v6.2.0)	Deleterious	Deleterious	–	Deleterious	Deleterious	–
Score	0.00	0.00	–	0.00	0.00	–
Align GVGD (v2007)	Benign	Likely benign	–	Damaging	Benign	–
Class	C0	C15	–	C65	C0	–
Grantham distance	Large	Moderate	–	Moderate	Small	–
gnomAD
Variant ID	16-1261968-G-C	16-1258048-G-A	Not reported	Not reported	Not reported	Not reported
Frequency all	0.0016%	0.0051%	None	None	None	None
EUR allele frequency	0.0035%	0.0075%	None	None	None	None
EUR carrier frequency	1 in 14,500	1 in 7000	None	None	None	None

Reference sequence NM_021098.3.

FS del, frameshift deletion.