. 2017 Jul 31;18(8):1665. doi: 10.3390/ijms18081665

Table 1.

Summary of GATM (glycine amidinotransferase) gene sequencing results. Variants identified in the autisim spectrum disorder (ASD) population are noted, and minor allele frequency (MAF) calculated. MAF of variants present in 1000 Genomes, Exome Sequencing Project (ESP) and Exome Aggregation Consortium (ExAC) databases are shown for comparison. ¹ Total number of samples = 166 (332 alleles); ² MAF = minor allele frequency; the number of alleles in which variant was found/total number of alleles; ³ MAC = minor allele count; the number of times the minor allele was observed in the sample population of chromosomes; ⁴ Polymorphic variant: (>0.01 MAF in one database); ⁵ Rare variant: ≤0.01 MAF in at least one published database; ⁶ Novel variant: Not present in any published database; coding sequence (exons) are in bold. SNP: single nucleotide polymorphism; UTR: untranslated region; and SIFT: ‘sorting tolerant from intolerant’ algorithm.

			Autism Population (n = 166, Alleles = 332 ¹)			Databases
GATM Exon/Intron	DNA Change/Protein Change	SNP ID	Homozygous/Heterozygous Change ¹	Number of Observed Alleles	MAF ²	1000 Genomes (Phase 3) MAF, MAC ³)	ESP Report (July 2013) MAF, MAC	ExAC (January 2015) MAF, MAC	Comments
5UTR	c. − 200C > T	rs7164139	Homo: 20	118	0.355	0.444	x	0.5533	polymorphic variant ⁴
			Hetero: 78			2223/5008		83/150
5UTR	c. − 140C > T	rs533626184	Hetero: 1	1	0.003	0.0022	x	x	rare variant
						11/5008
5UTR	c. − 30T > G	rs8024550	Hetero: 5	5	0.015	0.144	0.073	0.07742	polymorphic variant
						720/5008	651/8926	155/2002
intron 1	c.70 − 77C > T	rs12437887	Homo: 20	116	0.349	0.443	x	x	polymorphic variant
			Hetero: 76			2221/5008
intron 1	c.70 − 38G > T	rs12437840	Homo: 23	119	0.358	0.443	0.270	0.3827	polymorphic variant
			Hetero: 73			2219/5008	3509/12992	24153/63112
exon 2	c.282G > A	rs141223762	Hetero: 1	1	0.003	NA	0.000154	0.0001153	rare variant ⁵
	p.=						2/12992	14/121390
intron 2	c.289 − 76T > C	rs540536879	Hetero: 3	3	0.009	0.000998	x	x	rare variant
						5/5008
intron 2	c.289 − 34T > C	rs74009633	Hetero: 1	1	0.003	0.0096	0.005	0.001947	rare variant
						48/5008	65/12982	193/99144
intron 2	c.289 − 24G > A	rs145644806	Hetero: 1	1	0.003	0.0002	0.000154	x	rare variant
						1/5008	2/12988
exon 3	c.330A > T	rs1288775	Homo: 29	132	0.398	0.619	0.435	0.581	polymorphic variant
	p.Q110H		Hetero: 74			3098/5008	5651/12992	70416/121104
intron 3	c.485-11_dupT		Homo: 1	2	0.006	x	x	x	novel variant ⁶
exon 5	c.700G > C		Hetero: 1	1	0.003	NA	x	0.00001651	rare variant
	p.D234H							2/121104	SIFT: deleterious (score: 0); PolyPhen-2: probably damaging (score: 0.986); MutationTaster: disease-causing (p-value: 1.0)
intron 5	c.813 + 46C > G	rs150282769	Hetero: 1	1	0.003	0.0002	0.000847	0.0004	rare variant
						1/5008	11/12992	46/118404
intron 6	c.978 + 43T > C		Hetero: 1	1	0.003	x	x	x	novel variant
intron 6	c.979 − 316A > G	rs9972405	Homo: 1	40	0.120	0.0998	x	x	polymorphic variant
			Hetero: 38			500/5008
intron 6	c.979-49_979-51delTAA	rs200176845	Homo: 1	2	0.006	0.0100	0.0137	0.00228	rare variant
	c.979-49_979-51delTAA					50/5008	171/12480	248/108652
intron 6	c.979 − 39T > C		Hetero: 1	1	0.003	x	x	x	novel variant
intron 7	c.1043 − 254A > G	rs57369693	Homo: 1	40	0.120	0.0998	x	x	polymorphic variant
			Hetero: 38			500/5008
intron 8	c.1159 + 39A > G	rs113129788	Hetero: 1	1	0.003	0.0002	x	0.000019	rare variant
						1/5008		2/105236
intron 8	c.1160 − 46C > T	rs201589362	Hetero: 2	2	0.006	0.0002		0.00006987	rare variant
						1/5008		7/100180
exon 9	c.1252T > C	rs1145086	Homo: 46	172	0.518	0.2823	0.534	0.5329	polymorphic variant
	p.=		Hetero: 80			1414/5008	6937/12992	64562/121146
3UTR	c.*27C > G	rs200143728	Hetero: 1	1	0.003	NA	x	0.0004716	rare variant
								56/118754
3UTR	c.*125G > A	rs143689218	Hetero: 2	2	0.006	0.0086	x	x	rare variant
						43/5008
3UTR	c.*411G > A		Hetero: 1	1	0.003	x	x	x	novel variant
3UTR	c.*600A > G	rs1049503	Homo: 23	120	0.361	0.4507	x	x	polymorphic variant
			Hetero: 74			2257/5008
3UTR	c.*715T > C	rs1049508	Homo: 27	123	0.370	0.618	x	x	polymorphic variant
			Hetero: 69			3094/5008
3UTR	c.734_735insCA	rs35410548	Homo: 46	171	0.515	0.718	x	x	polymorphic variant
	c.734_735insCA		Hetero: 79			3594/5008
3UTR	c.*913G > A	rs17618637	Hetero: 10	10	0.030	0.0553	x	x	polymorphic variant
						277/5008
3UTR	c.*940C > T	rs1049518	Homo: 54	108	0.325	0.718	x	x	polymorphic variant
						3594/5008