Table 1

ALS-implicated variants identified among 616 Australian SALS cases

Gene name	Nucleotide alteration	Consequence	Frequency in SALS (n=616)		Association analysis (Fisher's exact test p value)
Gene name	Nucleotide alteration	Consequence	No. heterozygous cases	No. homozygous cases	SALS vs gnomAD non-neuro NFE	Project MiNE cases vs controls
ANG	c.A122T	p.K41I	2	0	1	.
ANG	c.A208G	p.I70V	1	0	1	.
ATXN2	CAG expansion (29–39 repeats)		10	0	N/A	N/A
C21orf2	c.G172T	p.V58L	22	1	0.0140124	.
C9orf72	GGGGCC repeat expansion (>30 repeats)		41	0	N/A	N/A
CCNF	c.T1810A	p.F604I	1	0	1	1
CCNF	c.G2140A	p.V714M	17	1	0.8111191	.
CHCHD10	c.C100T	p.P34S	6	0	0.6427256	.
CHCHD10	c.C239T	p.P80L	2	0	0.0377862	.
CHCHD10	c.T403C	p.Y135H	1	0	0.3094276	.
DCTN1	c.C3746T	p.T1249I	6	0	1	.
ELP3*	g.28086088G>A	Unknown	227	345	0.0433814	.
ELP3*	g.28136109T>C	Unknown	104	502	0.5108734	.
FUS	c.*41G>A	Unknown	12	0	0.4211107	.
FUS	c.833–29C>T	Unknown	15	1	0.9006159	.
GPX3-TNIP1*	c.*3144C>T	Unknown	248	315	0.0015471	.
NEFH	c.2230_2247del	Unknown	1	0	0.3617984	.
NEK1	c.G782A	p.R261H	3	0	0.6387112	.
*NEK1*	c.C3107G	p.S1036X	5	0	0.0000102	0.000647562
OPTN	c.T293A	p.M98K	26	2	0.4873868	.
OPTN	c.G403T	p.E135X	2	0	0.0188011	.
OPTN	c.G476T	p.G159V	1	0	0.0401598	.
SETX	c.A431G	p.N144S	1	0	0.0234651	.
SETX	c.G2755C	p.V919L	1	0	0.1432519	.
SETX	c.A2975G	p.K992R	10	0	0.0065459	.
SETX	c.C4433A	p.A1478E	1	0	0.4917794	.
SETX	c.T4660G	p.C1554G	1	0	0.1388244	.
SETX	c.T7640C	p.I2547T	8	0	0.7054959	.
SOD1	c.A272C	p.D91A	1	0	0.5323133	.
*SOD1*	c.T341C	p.I114T	3	0	0.0000099	0.189084762
SPG11	c.C491T	p.S164L	0	1	0.0071392	.
SPG11	c.A6224G	p.N2075S	5	0	1	.
SQSTM1	c.C98T	p.A33V	1	0	1	.
SQSTM1	c.A712G	p.K238E	7	0	0.2207281	.
SQSTM1	c.G822C	p.E274D	30	0	0.699596	.
SQSTM1	c.C1175T	p.P392L	3	0	0.2471604	.
SQSTM1	g.3'+7G>C	unknown	1	0	0.1246189
SQSTM1	g.5'−37C>T	unknown	1	0	0.510332
TARDBP	c.543+112C>A	unknown	2	0	1	.
TARDBP	c.G859A	p.G287S	1	0	0.0401616	.
TARDBP	c.G883A	p.G295S	1	0	0.0135711	.
TARDBP	c.G1144A	p.A382T	1	0	0.0292553	.
TARDBP	c.A1147G	p.I383V	2	0	0.000216	.
TBK1	c.A871G	p.K291E	1	0	0.2670662	.
TBK1	c.G1073A	p.R358H	1	0	0.0350117	.
UBQLN2	c.G1019T	p.S340I	1	0	0.0557581	.

Variants that were significantly associated with Australian SALS are indicated in bold.
*These variants had MAF >0.2 among gnomAD non-neuro NFE controls and were removed from further analysis as common variants.
gnomAD, Genome Aggregation Database; MAF, minor allele frequency; N/A, not available; NFE, non-Finnish European; SALS, sporadic amyotrophic lateral sclerosis.