Table 1.

Rare potentially deleterious coding variants identified at the TREM and MS4A loci among North American AD patients (N = 210) and controls (N = 233).

Chr	Location	dbSNP138	Ref	Alt	Gene	Transcript	Exon	Nucleotide	Amino acid change	Function
6	41117594	rs138237630	A	T	TREML1	NM_178174	6	c.T684A	p.D228E	Nonsynonymous
	41121999	rs201565463	G	A	TREML1	NM_178174	1	c.C28T	p.L10F	Nonsynonymous
	41126346	.	C	A	TREM2	NM_001271821	4	c.G655T	p.G219C	Nonsynonymous
	41126387	.	A	G	TREM2	NM_001271821	4	c.T614C	p.L205P	Nonsynonymous
	41127543	rs2234255	G	A	TREM2	NM_018965	3	c.C469T	p.H157Y	Nonsynonymous
	41129133	rs142232675	C	T	TREM2	NM_018965	2	c.G259A	p.D87N	Nonsynonymous
	41129178	.	G	C	TREM2	NM_018965	2	c.C214G	p.L72V	Nonsynonymous
	41129252	rs75932628	C	T	TREM2	NM_018965	2	c.G140A	p.R47H	Nonsynonymous
	41162204	rs115991880	G	T	TREML2	NM_024807	3	c.C744A	p.S248R	Nonsynonymous
	41166063	rs147506354	C	A	TREML2	NM_024807	2	c.G160T	p.V54F	Nonsynonymous
	41196683	rs373300218	C	G	TREML4	NM_198153	2	c.C295G	p.L99V	Nonsynonymous
	41204295	.	T	C	TREML4	NM_198153	5	c.T578C	p.L193P	Nonsynonymous
11	59829992	rs140838251	G	A	MS4A3	NM_006138	3	c.G208A	p.G70S	Nonsynonymous
	59857929	rs79741566	T	G	MS4A2	NM_000139	3	c.T307G	p.W103G	Nonsynonymous
	59861473	rs138180929	G	T	MS4A2	NM_000139	6	c.G574T	p.G192X	Stopgain
	59940500	rs138650483	C	T	MS4A6A	NM_001247999; NM_15285	7; 8	c.G736A; c.651þ1G>A	p.V246M	Nonsynonymous; splicing
	59947385	rs532381110	T	-	MS4A6A	NM_152852	4	c.201delA	p.A67fs	Frameshift deletion
	60064779	rs145442198	C	A	MS4A4A	NM_024021	4	c.C254A	p.T85K	Nonsynonymous
	60105214	.	G	C	MS4A6E	NM_139249	2	c.G148C	p.V50L	Nonsynonymous
	60160173	.	A	T	MS4A7	NM_206939	6	c.A562T	p.M188L	Nonsynonymous
	60160175	.	G	A	MS4A7	NM_206939	6	c.G564A	p.M188I	Nonsynonymous
	60160176	rs143858799	C	A	MS4A7	NM_206939	6	c.C565A	p.L189I	Nonsynonymous
	60161278	.	C	T	MS4A7	NM_206939	7	c.C667T	p.Q223X	Stopgain
	60183920	.	A	C	MS4A14	NM_001261828	6	c.A1578C	p.K526N	Nonsynonymous
	60184404	rs149015522	C	T	MS4A14	NM_001261828	6	c.C2062T	p.Q688X	Stopgain
	60184467	rs151183005	C	T	MS4A14	NM_001261828	6	c.C2125T	p.P709S	Nonsynonymous
	60233409	rs201245387	A	C	MS4A1	NM_152866	6	c.A352C	p.I118L	Nonsynonymous
	60309991	.	G	T	MS4A13	NM_001012417	7	c.403–1G>T	.	Splicing

Frequencies were checked at the 1000 Genomes project (general and European populations), as well as at the Exome Variant Server (data release ESP6500si v2) and Exome Aggregation Consortium (data release exac02). Variant effect on protein function was evaluated with the SIFT and Polyphen2 programs, and conservation scores were determined with GERPþþ. Key: AD, Alzheimer’s disease; FDR, false-positive discovery rates.