Table 2 Details of discovered rare mutations and in silico analyses

From: Rare loss of function mutations in N-methyl-d-aspartate glutamate receptors and their contributions to schizophrenia susceptibility

a
Chromosome	Position	Reference allele	Sample allele	Gene symbol	Phenotype	Protein variant	dbSNP ID	1000 Genomes frequency	NHLBI ESP frequency	HGVD frequency	iJGVD frequency	SIFT function prediction	PolyPhen-2 function prediction	MUTATIONTASTER function prediction	PRIMATE phcons	Primate phylop	Pedigree analysis
9	14,0052,907	G	A	GRIN1	SCZ	p.A349T; p.A370T	Rs148008303	0.0002	0.00006			Damaging	Possibly Damaging	disease causing	0.993	0.557
16	9,858,015	T	C	GRIN2A	SCZ	p.H1129R			0.000016			Tolerated	Benign	disease causing	0.074	0.525
16	9,858,403	C	T	GRIN2A	ASD	p.V1000M						Tolerated	Possibly Damaging	disease causing	0.959	0.651	inherited
16	9,858,511	G	C	GRIN2A	SCZ	p.Q964E			0.000032		0.0005	Tolerated	Benign	disease causing	0.983	0.651
16	9,858,751	C	T	GRIN2A	SCZ	p.D884N	Rs777684328	0.00002		0.0009	Damaging	Possibly Damaging	disease causing	0.994	0.651
16	9,858,774	A	G	GRIN2A	ASD	p.I876T	Rs199784503	0.0004	0.0003		0.0023	Tolerated	Probably Damaging	disease causing	0.965	0.53	inherited
16	9,862,785	G	A	GRIN2A	ASD	p.L840F	Rs371352783	0.00002			Damaging	Possibly Damaging	disease causing	0.997	0.559	inherited
16	9,927,969	T	G	GRIN2A	ASD	p.K590N			0.000033		0.0005	Tolerated	Benign	disease causing	0.985	0.525
16	9,943,618	T	G	GRIN2A	ASD	p.K441N						Tolerated	Benign	disease causing	0.995	0.525
16	10,032,377	G	A	GRIN2A	SCZ	p.A149V		0.04			0.0009	Tolerated	Probably Damaging	disease causing	0.956	0.559
16	10,032,405	G	C	GRIN2A	SCZ	p.P140A			0.000008		0.0009	Tolerated	Benign	disease causing	0.932	0.559
17	72,839,530	C	T	GRIN2C	ASD	p.A916T				0.0014	0.0005	Tolerated	Probably Damaging	disease causing	0.981	0.45	inherited
17	72,846,024	C	T	GRIN2C	ASD	p.E514K				0.0017		Tolerated	Possibly Damaging	disease causing	0.992	0.486
17	72,846,374	G	A	GRIN2C	SCZ	p.R488C	Rs186790306	0.0014	0.00007			Damaging	Probably Damaging	disease causing	0.994	0.486
17	72,846,483	C	G	GRIN2C	SCZ	p.K451N						Damaging	Probably Damaging	disease causing	0.722	−0.347
17	72,846,705	G	A	GRIN2C	ASD	p.H439Y						Tolerated	Benign	disease causing	0.015	0.557	inherited
17	72,846,800	G	A	GRIN2C	SCZ	p.T407M	Rs536926397	0.0002	0.00002			Damaging	Probably Damaging	disease causing	0.318	0.55

b
Chromosome	Position	Reference allele	Sample allele	Gene symbol	Phenotype	Protein cariant	dbSNP ID	1000 Genomes frequency	NHLBI ESP Frequency	HGVD Frequency	iJGVD Frequency	SIFT Function Prediction	PolyPhen-2 Function Prediction	MUTATIONTASTER Function Prediction	Primate PhCons	primate PhyloP	Pedigree analysis
17	72,850,836	GGGG		GRIN2C	SCZ	p.P132fs*59					NA	NA	disease causing	0.477	0.645
17	72,850,840	G	A	GRIN2C	ASD	p.T131I	Rs780165386	0.000009			Damaging	Possibly Damaging	disease causing	0.401	−0.176
17	72,851,093	G	A	GRIN2C	SCZ	p.R47C	Rs776102062	0.00003			Tolerated	Benign	disease causing	0.867	−0.276
19	48,908,432	G	A	GRIN2D	ASD	p.G303R						Tolerated	Possibly Damaging	disease causing	0.401	0.557	inherited
19	48,908,447	C	T	GRIN2D	SCZ	p.R308C	Rs746751166	0.00002			Tolerated	Benign	disease causing	0.989	0.557
19	48,917,841	G	A	GRIN2D	SCZ	p.S471N						Tolerated	Benign	disease causing	0.992	0.651
19	48,918,122	C	A	GRIN2D	SCZ	p.P472T						Tolerated	Possibly Damaging	disease causing	0.94	0.651
19	48,945,428	G	A	GRIN2D	SCZ	p.R821Q	Rs767410370	0.000008			Tolerated	Probably Damaging	disease causing	0.966	0.451
19	48,947,106	C	T	GRIN2D	ASD	p.P1308L				0.0049	0.0028	deleterious	NA	disease causing	0.038	0.466
9	104,375,732	C	A	GRIN3A	ASD	p.G898W					0.0005	Damaging	Probably Damaging	disease causing	0.948	0.651
9	104,433,232	T	C	GRIN3A	ASD/SCZ	p.K488E	Rs189425146 0.0042	0.42	0.0009		0.0009	Tolerated	Benign	disease causing	0.985	0.53	inherited
9	104,449,017	C	T	GRIN3A	SCZ	p.V389I	Rs200120504	0.0002		0.0005	Tolerated	Benign	disease causing	0.99	0.559
9	104,449,173	G	A	GRIN3A	ASD/SCZ	p.R337W	Rs773593066	0.00008	0.0017	0.0009	Damaging	Possibly Damaging	disease causing	0.971	0.559	inherited
9	104,499,853	G	T	GRIN3A	ASD	p.R137S	Rs769491656				Tolerated	Benign	disease causing	0.988	0.651	inherited
19	1,003,244	C	T	GRIN3B	SCZ	p.T181I	Rs540094501	0.0004	0.0002	0.0087	0.2924	Tolerated	Benign	disease causing	0.002	−0.397
19	1,003,255	G	A	GRIN3B	SCZ	p.G185S	Rs575985258	0.001	0.0006	0.0005	0.0005	Tolerated	Benign	disease causing	0.016	−0.397
19	1,003,721	G	A	GRIN3B	SCZ	p.R340Q	Rs577413695	0.0002				Tolerated	Benign	disease causing	0.652	0.459
19	1,004,573	G	A	GRIN3B	SCZ	p.G358D	Rs75047944	0.0006	0.0001	0.0044	0.0089	Damaging	Probably Damaging	disease causing	0.054	−0.524
19	1,004,998	G	A	GRIN3B	ASD/SCZ	p.V500M	Rs377572345	0.0001	0.0014		Damaging	Probably Damaging	disease causing	0.192	0.48
19	1,005,098	G	T	GRIN3B	ASD	p.S533I	Rs200427089	0.0004	0.0002	0.0036	0.002	Damaging	Possibly Damaging	disease causing	0.933	0.48	inherited
19	1,005,209	T	A	GRIN3B	SCZ	p.M570K	Rs750803476	0.0001			Tolerated	Possibly Damaging	disease causing	0.863	0.393
19	1,005,523	G	A	GRIN3B	SCZ	p.E675K	Rs759438437	0.000009	0.0005		Damaging	Probably Damaging	disease causing	0.026	−0.863
19	1,008,142	A	G	GRIN3B	SCZ	p.Y773C				0.0009		Tolerated	Probably Damaging	disease causing	0.081	−0.897

Genomic position is based on GRCh37/hg19
SNVsingle-nucleotide variant
dbSNP: dbSNP build 139 (http://www.ncbi.nlm.nih.gov/projects/SNP/); 1000 Genomes the 1000 Genomes Project (http://www.1000genomes.org), NHLBI Exome Aggregation Consortium (http://exac.broadinstitute.org), HGVD the Human Genetic Variation Database (http://www.genome.med.kyoto-u.ac.jp/SnpDB/), iJGVD Integrative Japanese Genome Variation (https://ijgvd.megabank.tohoku.ac.jp/)
SIFT (http://sift.jcvi.org/), PolyPhen-2 polymorphism phenotyping v.2 (http://genetics.bwh.harvard.edu/pph2/index.shtml). MUTATIONTASTER (http://www.mutationtaster.org/). PhastCons conservation score (http://compgen.cshl.edu/phast/phastCons-HOWTO.html): produces predictions of discrete conserved elements

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Table 2 Details of discovered rare mutations and in silico analyses

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