Skip to main page content
Accesskeys

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 Aliases 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.

rs4290270

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr12:72022455 (GRCh38.p12) 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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.42899 (107750/251170, GnomAD_exome)
A=0.44989 (56492/125568, TOPMED)
A=0.42681 (51779/121316, ExAC) (+ 8 more)
A=0.4560 (14282/31318, GnomAD)
A=0.4338 (5642/13006, GO-ESP)
T=0.487 (2440/5008, 1000G)
A=0.396 (1773/4480, Estonian)
A=0.344 (1326/3854, ALSPAC)
A=0.364 (1350/3708, TWINSUK)
T=0.45 (275/616, Vietnamese)
A=0.32 (190/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
TPH2 : Synonymous Variant
Publications
28 citations
Genomic View
See rs on genome
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.p12 chr 12 NC_000012.12:g.72022455A>T
GRCh37.p13 chr 12 NC_000012.11:g.72416235A>T
TPH2 RefSeqGene NG_008279.1:g.88610A>T
Gene: TPH2, tryptophan hydroxylase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TPH2 transcript NM_173353.4:c.1125A>T A [GCA] > A [GCT] Coding Sequence Variant
tryptophan 5-hydroxylase 2 NP_775489.2:p.Ala375= A (Ala) > A (Ala) Synonymous Variant
TPH2 transcript variant X1 XR_001748575.1:n. N/A Genic Downstream 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.

Allele: T (allele ID: 332804 )
ClinVar Accession Disease Names Clinical Significance
RCV000405228.1 Tryptophan 5-monooxygenase deficiency Likely-Benign
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
gnomAD - Exomes Global Study-wide 251170 A=0.42899 T=0.57101
gnomAD - Exomes European Sub 135170 A=0.37795 T=0.62205
gnomAD - Exomes Asian Sub 48990 A=0.4934 T=0.5066
gnomAD - Exomes American Sub 34550 A=0.4785 T=0.5215
gnomAD - Exomes African Sub 16256 A=0.5945 T=0.4055
gnomAD - Exomes Ashkenazi Jewish Sub 10072 A=0.3819 T=0.6181
gnomAD - Exomes Other Sub 6132 A=0.399 T=0.601
TopMed Global Study-wide 125568 A=0.44989 T=0.55011
ExAC Global Study-wide 121316 A=0.42681 T=0.57319
ExAC Europe Sub 73330 A=0.3730 T=0.6270
ExAC Asian Sub 25136 A=0.4922 T=0.5078
ExAC American Sub 11538 A=0.4797 T=0.5203
ExAC African Sub 10404 A=0.5892 T=0.4108
ExAC Other Sub 908 A=0.43 T=0.57
gnomAD - Genomes Global Study-wide 31318 A=0.4560 T=0.5440
gnomAD - Genomes European Sub 18866 A=0.3897 T=0.6103
gnomAD - Genomes African Sub 8690 A=0.592 T=0.408
gnomAD - Genomes East Asian Sub 1546 A=0.530 T=0.470
gnomAD - Genomes Other Sub 1080 A=0.421 T=0.579
gnomAD - Genomes American Sub 846 A=0.47 T=0.53
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=0.40 T=0.60
GO Exome Sequencing Project Global Study-wide 13006 A=0.4338 T=0.5662
GO Exome Sequencing Project European American Sub 8600 A=0.356 T=0.644
GO Exome Sequencing Project African American Sub 4406 A=0.585 T=0.415
1000Genomes Global Study-wide 5008 A=0.513 T=0.487
1000Genomes African Sub 1322 A=0.615 T=0.385
1000Genomes East Asian Sub 1008 A=0.534 T=0.466
1000Genomes Europe Sub 1006 A=0.377 T=0.623
1000Genomes South Asian Sub 978 A=0.49 T=0.51
1000Genomes American Sub 694 A=0.51 T=0.49
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.396 T=0.604
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.344 T=0.656
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.364 T=0.636
A Vietnamese Genetic Variation Database Global Study-wide 616 A=0.55 T=0.45
Northern Sweden ACPOP Study-wide 600 A=0.32 T=0.68
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 A= T Note
GRCh38.p12 chr 12 NC_000012.12:g.72022455= NC_000012.12:g.72022455A>T
GRCh37.p13 chr 12 NC_000012.11:g.72416235= NC_000012.11:g.72416235A>T
TPH2 RefSeqGene NG_008279.1:g.88610= NG_008279.1:g.88610A>T
TPH2 transcript NM_173353.4:c.1125= NM_173353.4:c.1125A>T
TPH2 transcript NM_173353.3:c.1125= NM_173353.3:c.1125A>T
tryptophan 5-hydroxylase 2 NP_775489.2:p.Ala375= NP_775489.2:p.Ala375=
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#.

81 SubSNP, 11 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss5678009 Feb 20, 2003 (111)
2 SC_SNP ss15529693 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss16596386 Feb 27, 2004 (120)
4 HG_BONN_CNS_SNPS ss28447414 Sep 20, 2004 (123)
5 ABI ss38936629 Mar 13, 2006 (126)
6 ILLUMINA ss65734662 Oct 16, 2006 (127)
7 HGSV ss84589973 Dec 14, 2007 (130)
8 BCMHGSC_JDW ss89239616 Mar 24, 2008 (129)
9 BGI ss103059454 Dec 01, 2009 (131)
10 1000GENOMES ss112143472 Jan 25, 2009 (130)
11 ENSEMBL ss133239843 Dec 01, 2009 (131)
12 ENSEMBL ss142780950 Dec 01, 2009 (131)
13 GMI ss157629261 Dec 01, 2009 (131)
14 SEATTLESEQ ss159726837 Dec 01, 2009 (131)
15 ILLUMINA ss160670420 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss168496108 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss175181093 Jul 04, 2010 (132)
18 BUSHMAN ss198379637 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss208318637 Jul 04, 2010 (132)
20 1000GENOMES ss211302992 Jul 14, 2010 (132)
21 1000GENOMES ss225824408 Jul 14, 2010 (132)
22 1000GENOMES ss235986680 Jul 15, 2010 (132)
23 1000GENOMES ss242536191 Jul 15, 2010 (132)
24 GMI ss281450934 May 04, 2012 (137)
25 GMI ss286584617 Apr 25, 2013 (138)
26 PJP ss291279702 May 09, 2011 (134)
27 NHLBI-ESP ss342362429 May 09, 2011 (134)
28 ILLUMINA ss481896339 Sep 08, 2015 (146)
29 ILLUMINA ss483103973 May 04, 2012 (137)
30 ILLUMINA ss483858389 May 04, 2012 (137)
31 1000GENOMES ss491047539 May 04, 2012 (137)
32 CLINSEQ_SNP ss491669261 May 04, 2012 (137)
33 ILLUMINA ss536053960 Sep 08, 2015 (146)
34 TISHKOFF ss563247713 Apr 25, 2013 (138)
35 SSMP ss658813653 Apr 25, 2013 (138)
36 ILLUMINA ss779518704 Aug 21, 2014 (142)
37 ILLUMINA ss782372778 Aug 21, 2014 (142)
38 ILLUMINA ss834989158 Aug 21, 2014 (142)
39 JMKIDD_LAB ss974484450 Aug 21, 2014 (142)
40 EVA-GONL ss989678644 Aug 21, 2014 (142)
41 JMKIDD_LAB ss1067536021 Aug 21, 2014 (142)
42 JMKIDD_LAB ss1078565810 Aug 21, 2014 (142)
43 1000GENOMES ss1345574951 Aug 21, 2014 (142)
44 DDI ss1426976462 Apr 01, 2015 (144)
45 EVA_GENOME_DK ss1576366367 Apr 01, 2015 (144)
46 EVA_FINRISK ss1584083328 Apr 01, 2015 (144)
47 EVA_DECODE ss1599357998 Apr 01, 2015 (144)
48 EVA_UK10K_ALSPAC ss1628881933 Apr 01, 2015 (144)
49 EVA_UK10K_TWINSUK ss1671875966 Apr 01, 2015 (144)
50 EVA_EXAC ss1691018634 Apr 01, 2015 (144)
51 EVA_MGP ss1711336567 Apr 01, 2015 (144)
52 HAMMER_LAB ss1807306368 Sep 08, 2015 (146)
53 WEILL_CORNELL_DGM ss1933042013 Feb 12, 2016 (147)
54 GENOMED ss1967621379 Jul 19, 2016 (147)
55 JJLAB ss2027272112 Sep 14, 2016 (149)
56 USC_VALOUEV ss2155615573 Dec 20, 2016 (150)
57 HUMAN_LONGEVITY ss2190939345 Dec 20, 2016 (150)
58 TOPMED ss2354919735 Dec 20, 2016 (150)
59 SYSTEMSBIOZJU ss2628118691 Nov 08, 2017 (151)
60 ILLUMINA ss2632976839 Nov 08, 2017 (151)
61 GRF ss2699965398 Nov 08, 2017 (151)
62 ILLUMINA ss2710765246 Nov 08, 2017 (151)
63 GNOMAD ss2739988856 Nov 08, 2017 (151)
64 GNOMAD ss2748917895 Nov 08, 2017 (151)
65 GNOMAD ss2912126019 Nov 08, 2017 (151)
66 AFFY ss2985621391 Nov 08, 2017 (151)
67 SWEGEN ss3009919528 Nov 08, 2017 (151)
68 EVA_SAMSUNG_MC ss3023067945 Nov 08, 2017 (151)
69 BIOINF_KMB_FNS_UNIBA ss3027446032 Nov 08, 2017 (151)
70 TOPMED ss3174611673 Nov 08, 2017 (151)
71 CSHL ss3350128550 Nov 08, 2017 (151)
72 ILLUMINA ss3626910529 Oct 12, 2018 (152)
73 ILLUMINA ss3630985031 Oct 12, 2018 (152)
74 ILLUMINA ss3636197588 Oct 12, 2018 (152)
75 OMUKHERJEE_ADBS ss3646444812 Oct 12, 2018 (152)
76 URBANLAB ss3649868095 Oct 12, 2018 (152)
77 EGCUT_WGS ss3677191606 Jul 13, 2019 (153)
78 EVA_DECODE ss3693945115 Jul 13, 2019 (153)
79 ACPOP ss3739144063 Jul 13, 2019 (153)
80 EVA ss3750647160 Jul 13, 2019 (153)
81 KHV_HUMAN_GENOMES ss3815981171 Jul 13, 2019 (153)
82 1000Genomes NC_000012.11 - 72416235 Oct 12, 2018 (152)
83 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 72416235 Oct 12, 2018 (152)
84 Genetic variation in the Estonian population NC_000012.11 - 72416235 Oct 12, 2018 (152)
85 ExAC NC_000012.11 - 72416235 Oct 12, 2018 (152)
86 gnomAD - Genomes NC_000012.11 - 72416235 Jul 13, 2019 (153)
87 gnomAD - Exomes NC_000012.11 - 72416235 Jul 13, 2019 (153)
88 GO Exome Sequencing Project NC_000012.11 - 72416235 Oct 12, 2018 (152)
89 Northern Sweden NC_000012.11 - 72416235 Jul 13, 2019 (153)
90 TopMed NC_000012.12 - 72022455 Oct 12, 2018 (152)
91 UK 10K study - Twins NC_000012.11 - 72416235 Oct 12, 2018 (152)
92 A Vietnamese Genetic Variation Database NC_000012.11 - 72416235 Jul 13, 2019 (153)
93 ClinVar RCV000405228.1 Oct 12, 2018 (152)
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).

Associated ID History Updated (Build)
rs57072898 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84589973 NC_000012.9:70702501:A:T NC_000012.12:72022454:A:T (self)
ss89239616, ss112143472, ss160670420, ss168496108, ss175181093, ss198379637, ss208318637, ss211302992, ss281450934, ss286584617, ss291279702, ss483103973, ss491669261, ss1599357998 NC_000012.10:70702501:A:T NC_000012.12:72022454:A:T (self)
58344978, 32396046, 22929854, 1324429, 159260298, 9224561, 1209472, 12428928, 32396046, 7189490, ss225824408, ss235986680, ss242536191, ss342362429, ss481896339, ss483858389, ss491047539, ss536053960, ss563247713, ss658813653, ss779518704, ss782372778, ss834989158, ss974484450, ss989678644, ss1067536021, ss1078565810, ss1345574951, ss1426976462, ss1576366367, ss1584083328, ss1628881933, ss1671875966, ss1691018634, ss1711336567, ss1807306368, ss1933042013, ss1967621379, ss2027272112, ss2155615573, ss2354919735, ss2628118691, ss2632976839, ss2699965398, ss2710765246, ss2739988856, ss2748917895, ss2912126019, ss2985621391, ss3009919528, ss3023067945, ss3350128550, ss3626910529, ss3630985031, ss3636197588, ss3646444812, ss3677191606, ss3739144063, ss3750647160 NC_000012.11:72416234:A:T NC_000012.12:72022454:A:T (self)
RCV000405228.1, 86874560, ss2190939345, ss3027446032, ss3174611673, ss3649868095, ss3693945115, ss3815981171 NC_000012.12:72022454:A:T NC_000012.12:72022454:A:T (self)
ss15529693, ss16596386 NT_029419.10:34559540:A:T NC_000012.12:72022454:A:T (self)
ss5678009, ss28447414, ss38936629, ss65734662, ss103059454, ss133239843, ss142780950, ss157629261, ss159726837 NT_029419.12:34559540:A:T NC_000012.12:72022454:A:T (self)
Help

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

28 citations for rs4290270
PMID Title Author Year Journal
17167340 Polymorphisms in the neuronal isoform of tryptophan hydroxylase 2 are associated with bipolar disorder in French Canadian pedigrees. Harvey M et al. 2007 Psychiatric genetics
17453063 Tryptophan hydroxylase 2 (TPH2) haplotypes predict levels of TPH2 mRNA expression in human pons. Lim JE et al. 2007 Molecular psychiatry
18181017 TPH2 and TPH1: association of variants and interactions with heroin addiction. Nielsen DA et al. 2008 Behavior genetics
18698231 Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. Johnson AD et al. 2008 Pharmacogenetics and genomics
19352219 Support for tryptophan hydroxylase-2 as a susceptibility gene for bipolar affective disorder. Roche S et al. 2009 Psychiatric genetics
19693267 Financial and psychological risk attitudes associated with two single nucleotide polymorphisms in the nicotine receptor (CHRNA4) gene. Roe BE et al. 2009 PloS one
19763617 Involvement of tryptophan hydroxylase 2 (TPH2) gene polymorphisms in susceptibility to coronary artery lesions in Korean children with Kawasaki disease. Park SW et al. 2010 European journal of pediatrics
20126463 Alternative splicing and extensive RNA editing of human TPH2 transcripts. Grohmann M et al. 2010 PloS one
20201854 Search for genetic markers and functional variants involved in the development of opiate and cocaine addiction and treatment. Yuferov V et al. 2010 Annals of the New York Academy of Sciences
20938755 Association study of tryptophan hydroxylase-2 gene in schizophrenia and its clinical features in Chinese Han population. Zhang C et al. 2011 Journal of molecular neuroscience
21172166 Pharmacogenetics of antidepressant response. Porcelli S et al. 2011 Journal of psychiatry & neuroscience
21289622 Pharmacogenomics of the RNA world: structural RNA polymorphisms in drug therapy. Sadee W et al. 2011 Clinical pharmacology and therapeutics
21620479 Tryptophan hydroxylase 2 gene is associated with major depressive disorder in a female Chinese population. Shen X et al. 2011 Journal of affective disorders
21886586 Association analysis of the tryptophan hydroxylase 2 gene polymorphisms in patients with methamphetamine dependence/psychosis. Kobayashi H et al. 2011 Current neuropharmacology
21937687 Influence and interaction of genetic polymorphisms in the serotonin system and life stress on antidepressant drug response. Xu Z et al. 2012 Journal of psychopharmacology (Oxford, England)
22655589 Investigation of tryptophan hydroxylase 2 (TPH2) in schizophrenia and in the response to antipsychotics. Schuhmacher A et al. 2012 Journal of psychiatric research
23300701 Genome-wide search for gene-gene interactions in colorectal cancer. Jiao S et al. 2012 PloS one
23628433 Genetic association and gene-gene interaction analyses suggest likely involvement of ITGB3 and TPH2 with autism spectrum disorder (ASD) in the Indian population. Singh AS et al. 2013 Progress in neuro-psychopharmacology & biological psychiatry
24881125 From pharmacogenetics to pharmacogenomics: the way toward the personalization of antidepressant treatment. Fabbri C et al. 2014 Canadian journal of psychiatry. Revue canadienne de psychiatrie
26028568 Association analysis of TPH-1 and TPH-2 genes with suicidal behavior in patients with attempted suicide in Mexican population. López-Narváez ML et al. 2015 Comprehensive psychiatry
26057341 Tryptophan hydroxylase 2 gene is associated with cognition in late-onset depression in a Chinese Han population. Wang X et al. 2015 Neuroscience letters
26232682 Genetic variability in tryptophan hydroxylase 2 gene in alcohol dependence and alcohol-related psychopathological symptoms. Plemenitaš A et al. 2015 Neuroscience letters
27521242 TPH-2 Polymorphisms Interact with Early Life Stress to Influence Response to Treatment with Antidepressant Drugs. Xu Z et al. 2016 The international journal of neuropsychopharmacology
28084537 Effect of childhood general traumas on suicide attempt depends on TPH2 and ADARB1 variants in psychiatric patients. Karanović J et al. 2017 Journal of neural transmission (Vienna, Austria
28590957 Genetic moderation of cocaine subjective effects by variation in the TPH1, TPH2, and SLC6A4 serotonin genes. Patriquin MA et al. 2017 Psychiatric genetics
29775696 TPH2 polymorphisms across the spectrum of psychiatric morbidity: A systematic review and meta-analysis. Ottenhof KW et al. 2018 Neuroscience and biobehavioral reviews
29952309 The Relationship Between Tryptophan Hydroxylase-2 Gene with Primary Insomnia and Depressive Symptoms in the Han Chinese Population Mei F et al. 2018 Balkan medical journal
30519155 TPH-2 Gene Polymorphism in Major Depressive Disorder Patients With Early-Wakening Symptom. Tao S et al. 2018 Frontiers in neuroscience

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.post308+0fe9b3b