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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs4354668

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:35419429 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>A / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.432283 (114421/264690, TOPMED)
T=0.456721 (63962/140046, GnomAD)
T=0.22341 (6311/28248, 14KJPN) (+ 14 more)
G=0.46903 (10980/23410, ALFA)
T=0.22949 (3844/16750, 8.3KJPN)
T=0.3768 (2413/6404, 1000G_30x)
T=0.3804 (1905/5008, 1000G)
G=0.4112 (1842/4480, Estonian)
G=0.3980 (1534/3854, ALSPAC)
G=0.4223 (1566/3708, TWINSUK)
T=0.2888 (844/2922, KOREAN)
G=0.318 (191/600, NorthernSweden)
T=0.257 (112/436, SGDP_PRJ)
T=0.389 (84/216, Qatari)
T=0.340 (72/212, Vietnamese)
T=0.36 (15/42, Siberian)
G=0.42 (17/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC1A2 : Intron Variant
Publications
7 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315
Population Group Sample Size Ref Allele Alt Allele
Total Global 23410 T=0.53097 G=0.46903
European Sub 18770 T=0.58924 G=0.41076
African Sub 2946 T=0.2251 G=0.7749
African Others Sub 114 T=0.123 G=0.877
African American Sub 2832 T=0.2292 G=0.7708
Asian Sub 112 T=0.312 G=0.688
East Asian Sub 86 T=0.29 G=0.71
Other Asian Sub 26 T=0.38 G=0.62
Latin American 1 Sub 146 T=0.418 G=0.582
Latin American 2 Sub 610 T=0.375 G=0.625
South Asian Sub 98 T=0.52 G=0.48
Other Sub 728 T=0.455 G=0.545


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 T=0.432283 G=0.567717
gnomAD - Genomes Global Study-wide 140046 T=0.456721 G=0.543279
gnomAD - Genomes European Sub 75796 T=0.59568 G=0.40432
gnomAD - Genomes African Sub 42016 T=0.22989 G=0.77011
gnomAD - Genomes American Sub 13650 T=0.41363 G=0.58637
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.4801 G=0.5199
gnomAD - Genomes East Asian Sub 3116 T=0.2882 G=0.7118
gnomAD - Genomes Other Sub 2148 T=0.4725 G=0.5275
14KJPN JAPANESE Study-wide 28248 T=0.22341 G=0.77659
Allele Frequency Aggregator Total Global 23410 T=0.53097 G=0.46903
Allele Frequency Aggregator European Sub 18770 T=0.58924 G=0.41076
Allele Frequency Aggregator African Sub 2946 T=0.2251 G=0.7749
Allele Frequency Aggregator Other Sub 728 T=0.455 G=0.545
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.375 G=0.625
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.418 G=0.582
Allele Frequency Aggregator Asian Sub 112 T=0.312 G=0.688
Allele Frequency Aggregator South Asian Sub 98 T=0.52 G=0.48
8.3KJPN JAPANESE Study-wide 16750 T=0.22949 G=0.77051
1000Genomes_30x Global Study-wide 6404 T=0.3768 G=0.6232
1000Genomes_30x African Sub 1786 T=0.1764 G=0.8236
1000Genomes_30x Europe Sub 1266 T=0.5845 G=0.4155
1000Genomes_30x South Asian Sub 1202 T=0.5333 G=0.4667
1000Genomes_30x East Asian Sub 1170 T=0.2821 G=0.7179
1000Genomes_30x American Sub 980 T=0.395 G=0.605
1000Genomes Global Study-wide 5008 T=0.3804 G=0.6196
1000Genomes African Sub 1322 T=0.1800 G=0.8200
1000Genomes East Asian Sub 1008 T=0.2708 G=0.7292
1000Genomes Europe Sub 1006 T=0.5855 G=0.4145
1000Genomes South Asian Sub 978 T=0.539 G=0.461
1000Genomes American Sub 694 T=0.401 G=0.599
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.5888 G=0.4112
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.6020 G=0.3980
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.5777 G=0.4223
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.2888 A=0.0000, G=0.7112
Northern Sweden ACPOP Study-wide 600 T=0.682 G=0.318
SGDP_PRJ Global Study-wide 436 T=0.257 G=0.743
Qatari Global Study-wide 216 T=0.389 G=0.611
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.340 G=0.660
Siberian Global Study-wide 42 T=0.36 G=0.64
The Danish reference pan genome Danish Study-wide 40 T=0.57 G=0.42
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 11 NC_000011.10:g.35419429T>A
GRCh38.p14 chr 11 NC_000011.10:g.35419429T>G
GRCh37.p13 chr 11 NC_000011.9:g.35440976T>A
GRCh37.p13 chr 11 NC_000011.9:g.35440976T>G
SLC1A2 RefSeqGene NG_008727.2:g.5130A>T
SLC1A2 RefSeqGene NG_008727.2:g.5130A>C
Gene: SLC1A2, solute carrier family 1 member 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC1A2 transcript variant 2 NM_001195728.3:c.-130+507…

NM_001195728.3:c.-130+507A>T

N/A Intron Variant
SLC1A2 transcript variant 3 NM_001252652.2:c.-167+479…

NM_001252652.2:c.-167+479A>T

N/A Intron Variant
SLC1A2 transcript variant 1 NM_004171.4:c.-463= N/A 5 Prime UTR Variant
SLC1A2 transcript variant X4 XM_011520285.2:c.5+507A>T N/A Intron Variant
SLC1A2 transcript variant X6 XM_017018137.2:c.-11+479A…

XM_017018137.2:c.-11+479A>T

N/A Intron Variant
SLC1A2 transcript variant X7 XM_017018138.2:c.-11+491A…

XM_017018138.2:c.-11+491A>T

N/A Intron Variant
SLC1A2 transcript variant X11 XM_047427443.1:c.-11+1058…

XM_047427443.1:c.-11+1058A>T

N/A Intron Variant
SLC1A2 transcript variant X9 XM_017018139.2:c.-463= N/A 5 Prime UTR Variant
SLC1A2 transcript variant X3 XM_017018136.1:c. N/A Genic Upstream Transcript Variant
SLC1A2 transcript variant X1 XM_047427436.1:c. N/A Genic Upstream Transcript Variant
SLC1A2 transcript variant X2 XM_047427437.1:c. N/A Genic Upstream Transcript Variant
SLC1A2 transcript variant X5 XM_047427438.1:c. N/A Genic Upstream Transcript Variant
SLC1A2 transcript variant X8 XM_047427440.1:c. N/A Genic Upstream Transcript Variant
SLC1A2 transcript variant X12 XM_047427441.1:c. N/A Genic Upstream Transcript Variant
SLC1A2 transcript variant X10 XM_047427442.1:c. N/A Genic Upstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= A G
GRCh38.p14 chr 11 NC_000011.10:g.35419429= NC_000011.10:g.35419429T>A NC_000011.10:g.35419429T>G
GRCh37.p13 chr 11 NC_000011.9:g.35440976= NC_000011.9:g.35440976T>A NC_000011.9:g.35440976T>G
SLC1A2 RefSeqGene NG_008727.2:g.5130= NG_008727.2:g.5130A>T NG_008727.2:g.5130A>C
SLC1A2 transcript variant 1 NM_004171.4:c.-463= NM_004171.4:c.-463A>T NM_004171.4:c.-463A>C
SLC1A2 transcript variant 1 NM_004171.3:c.-463= NM_004171.3:c.-463A>T NM_004171.3:c.-463A>C
SLC1A2 transcript variant X9 XM_017018139.2:c.-463= XM_017018139.2:c.-463A>T XM_017018139.2:c.-463A>C
SLC1A2 transcript variant 2 NM_001195728.2:c.-130+507= NM_001195728.2:c.-130+507A>T NM_001195728.2:c.-130+507A>C
SLC1A2 transcript variant 2 NM_001195728.3:c.-130+507= NM_001195728.3:c.-130+507A>T NM_001195728.3:c.-130+507A>C
SLC1A2 transcript variant 3 NM_001252652.1:c.-167+479= NM_001252652.1:c.-167+479A>T NM_001252652.1:c.-167+479A>C
SLC1A2 transcript variant 3 NM_001252652.2:c.-167+479= NM_001252652.2:c.-167+479A>T NM_001252652.2:c.-167+479A>C
SLC1A2 transcript variant X4 XM_011520285.2:c.5+507= XM_011520285.2:c.5+507A>T XM_011520285.2:c.5+507A>C
SLC1A2 transcript variant X6 XM_017018137.2:c.-11+479= XM_017018137.2:c.-11+479A>T XM_017018137.2:c.-11+479A>C
SLC1A2 transcript variant X7 XM_017018138.2:c.-11+491= XM_017018138.2:c.-11+491A>T XM_017018138.2:c.-11+491A>C
SLC1A2 transcript variant X11 XM_047427443.1:c.-11+1058= XM_047427443.1:c.-11+1058A>T XM_047427443.1:c.-11+1058A>C
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

65 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss5797151 Feb 20, 2003 (111)
2 ABI ss40063302 Mar 14, 2006 (126)
3 BGI ss106735840 Feb 04, 2009 (130)
4 COMPLETE_GENOMICS ss168199263 Jul 04, 2010 (132)
5 BUSHMAN ss202583950 Jul 04, 2010 (132)
6 1000GENOMES ss235518701 Jul 15, 2010 (132)
7 1000GENOMES ss242158965 Jul 15, 2010 (132)
8 BL ss255042667 May 09, 2011 (134)
9 GMI ss280957305 May 04, 2012 (137)
10 ILLUMINA ss482822832 May 04, 2012 (137)
11 ILLUMINA ss483840034 May 04, 2012 (137)
12 SSMP ss657989867 Apr 25, 2013 (138)
13 ILLUMINA ss782363577 Sep 08, 2015 (146)
14 EVA-GONL ss988401115 Aug 21, 2014 (142)
15 1000GENOMES ss1340820068 Aug 21, 2014 (142)
16 DDI ss1426599349 Apr 01, 2015 (144)
17 EVA_GENOME_DK ss1575643971 Apr 01, 2015 (144)
18 EVA_DECODE ss1598077787 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1626363378 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1669357411 Apr 01, 2015 (144)
21 WEILL_CORNELL_DGM ss1931759909 Feb 12, 2016 (147)
22 ILLUMINA ss1959340140 Feb 12, 2016 (147)
23 JJLAB ss2026627276 Sep 14, 2016 (149)
24 CSHL ss2136777916 Nov 08, 2017 (151)
25 USC_VALOUEV ss2154916818 Dec 20, 2016 (150)
26 HUMAN_LONGEVITY ss2181637307 Dec 20, 2016 (150)
27 SYSTEMSBIOZJU ss2627787917 Nov 08, 2017 (151)
28 ILLUMINA ss2632824149 Nov 08, 2017 (151)
29 GRF ss2699197003 Nov 08, 2017 (151)
30 ILLUMINA ss2710733296 Nov 08, 2017 (151)
31 GNOMAD ss2898310904 Nov 08, 2017 (151)
32 AFFY ss2985584858 Nov 08, 2017 (151)
33 SWEGEN ss3007883777 Nov 08, 2017 (151)
34 ILLUMINA ss3021325286 Nov 08, 2017 (151)
35 BIOINF_KMB_FNS_UNIBA ss3027113058 Nov 08, 2017 (151)
36 CSHL ss3349540334 Nov 08, 2017 (151)
37 ILLUMINA ss3639794239 Oct 12, 2018 (152)
38 ILLUMINA ss3641730049 Oct 12, 2018 (152)
39 ILLUMINA ss3651688694 Oct 12, 2018 (152)
40 EGCUT_WGS ss3675290162 Jul 13, 2019 (153)
41 EVA_DECODE ss3691563331 Jul 13, 2019 (153)
42 ACPOP ss3738081068 Jul 13, 2019 (153)
43 EVA ss3749159242 Jul 13, 2019 (153)
44 KHV_HUMAN_GENOMES ss3814508586 Jul 13, 2019 (153)
45 EVA ss3825796208 Apr 26, 2020 (154)
46 EVA ss3832574093 Apr 26, 2020 (154)
47 EVA ss3839838233 Apr 26, 2020 (154)
48 EVA ss3845315928 Apr 26, 2020 (154)
49 SGDP_PRJ ss3876016050 Apr 26, 2020 (154)
50 KRGDB ss3924274080 Apr 26, 2020 (154)
51 FSA-LAB ss3984000073 Apr 26, 2021 (155)
52 EVA ss3986054429 Apr 26, 2021 (155)
53 TOPMED ss4881344000 Apr 26, 2021 (155)
54 TOMMO_GENOMICS ss5201468172 Apr 26, 2021 (155)
55 1000G_HIGH_COVERAGE ss5287013643 Oct 16, 2022 (156)
56 EVA ss5398860251 Oct 16, 2022 (156)
57 HUGCELL_USP ss5482253790 Oct 16, 2022 (156)
58 1000G_HIGH_COVERAGE ss5582458785 Oct 16, 2022 (156)
59 SANFORD_IMAGENETICS ss5650990865 Oct 16, 2022 (156)
60 TOMMO_GENOMICS ss5748444943 Oct 16, 2022 (156)
61 YY_MCH ss5812283736 Oct 16, 2022 (156)
62 EVA ss5836504503 Oct 16, 2022 (156)
63 EVA ss5849936754 Oct 16, 2022 (156)
64 EVA ss5919534667 Oct 16, 2022 (156)
65 EVA ss5942306191 Oct 16, 2022 (156)
66 1000Genomes NC_000011.9 - 35440976 Oct 12, 2018 (152)
67 1000Genomes_30x NC_000011.10 - 35419429 Oct 16, 2022 (156)
68 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 35440976 Oct 12, 2018 (152)
69 Genetic variation in the Estonian population NC_000011.9 - 35440976 Oct 12, 2018 (152)
70 The Danish reference pan genome NC_000011.9 - 35440976 Apr 26, 2020 (154)
71 gnomAD - Genomes NC_000011.10 - 35419429 Apr 26, 2021 (155)
72 KOREAN population from KRGDB NC_000011.9 - 35440976 Apr 26, 2020 (154)
73 Northern Sweden NC_000011.9 - 35440976 Jul 13, 2019 (153)
74 Qatari NC_000011.9 - 35440976 Apr 26, 2020 (154)
75 SGDP_PRJ NC_000011.9 - 35440976 Apr 26, 2020 (154)
76 Siberian NC_000011.9 - 35440976 Apr 26, 2020 (154)
77 8.3KJPN NC_000011.9 - 35440976 Apr 26, 2021 (155)
78 14KJPN NC_000011.10 - 35419429 Oct 16, 2022 (156)
79 TopMed NC_000011.10 - 35419429 Apr 26, 2021 (155)
80 UK 10K study - Twins NC_000011.9 - 35440976 Oct 12, 2018 (152)
81 A Vietnamese Genetic Variation Database NC_000011.9 - 35440976 Jul 13, 2019 (153)
82 ALFA NC_000011.10 - 35419429 Apr 26, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
31451474, ss3924274080 NC_000011.9:35440975:T:A NC_000011.10:35419428:T:A (self)
ss168199263, ss202583950, ss255042667, ss280957305, ss482822832, ss1598077787, ss2136777916, ss3639794239 NC_000011.8:35397551:T:G NC_000011.10:35419428:T:G (self)
53328684, 29627164, 21028410, 2520512, 31451474, 11365933, 13801839, 28033030, 7433172, 59437479, 29627164, 6580892, ss235518701, ss242158965, ss483840034, ss657989867, ss782363577, ss988401115, ss1340820068, ss1426599349, ss1575643971, ss1626363378, ss1669357411, ss1931759909, ss1959340140, ss2026627276, ss2154916818, ss2627787917, ss2632824149, ss2699197003, ss2710733296, ss2898310904, ss2985584858, ss3007883777, ss3021325286, ss3349540334, ss3641730049, ss3651688694, ss3675290162, ss3738081068, ss3749159242, ss3825796208, ss3832574093, ss3839838233, ss3876016050, ss3924274080, ss3984000073, ss3986054429, ss5201468172, ss5398860251, ss5650990865, ss5836504503, ss5942306191 NC_000011.9:35440975:T:G NC_000011.10:35419428:T:G (self)
69984720, 376426225, 82282047, 96889656, 2931053592, ss2181637307, ss3027113058, ss3691563331, ss3814508586, ss3845315928, ss4881344000, ss5287013643, ss5482253790, ss5582458785, ss5748444943, ss5812283736, ss5849936754, ss5919534667 NC_000011.10:35419428:T:G NC_000011.10:35419428:T:G (self)
ss5797151, ss40063302, ss106735840 NT_009237.18:35380975:T:G NC_000011.10:35419428:T:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

7 citations for rs4354668
PMID Title Author Year Journal
22728822 Cognitive dysfunction and glutamate reuptake: effect of EAAT2 polymorphism in schizophrenia. Spangaro M et al. 2012 Neuroscience letters
25406999 Association of rare variation in the glutamate receptor gene SLC1A2 with susceptibility to bipolar disorder and schizophrenia. Fiorentino A et al. 2015 European journal of human genetics
26459047 Common variants in SLC1A2 and schizophrenia: Association and cognitive function in patients with schizophrenia and healthy individuals. Zhang B et al. 2015 Schizophrenia research
28277565 Pharmacogenetic Analysis of Functional Glutamate System Gene Variants and Clinical Response to Clozapine. Taylor DL et al. 2017 Molecular neuropsychiatry
29790085 White Matter Microstructure in Bipolar Disorder Is Influenced by the Interaction between a Glutamate Transporter EAAT1 Gene Variant and Early Stress. Poletti S et al. 2019 Molecular neurobiology
30539765 Neurobiology of cognitive remediation in schizophrenia: Effects of EAAT2 polymorphism. Spangaro M et al. 2018 Schizophrenia research
31118638 Association study of the excitatory amino acid transporter 2 (EAAT2) and glycine transporter 1 (GlyT1) gene polymorphism with schizophrenia in a Polish population. Merk W et al. 2019 Neuropsychiatric disease and treatment
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post774+babeb33