chr1:19666020:C>T Detail (hg38) (HTR6)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr1:19,992,513-19,992,513 View the variant detail on this assembly version. |
| hg38 | chr1:19,666,020-19,666,020 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000871.2:c.267C>T | NP_000862.1:p.Tyr89= |
| Ensemble | ENST00000289753.2:c.267C>T | ENST00000289753.2:p.Tyr89= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.299 |
| ToMMo:0.299 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.237 |
Prediction
ClinVar
| Clinical Significance | |
| Review star | [No Data.] |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.011 | Unipolar Depression | In this study, we evaluated the association of seven serotonin signal transducti... | BeFree | 19590397 | Detail |
| 0.155 | major depressive disorder | In this study, we evaluated the association of seven serotonin signal transducti... | BeFree | 19590397 | Detail |
| <0.001 | dementia | In order to identify gene variants related to the serotonergic neurotransmitter ... | BeFree | 11725820 | Detail |
| <0.001 | Presenile dementia | In order to identify gene variants related to the serotonergic neurotransmitter ... | BeFree | 11725820 | Detail |
| <0.001 | Presenile dementia | In order to identify gene variants related to the serotonergic neurotransmitter ... | BeFree | 11725820 | Detail |
| <0.001 | Unipolar Depression | Association between the 5-HT6 receptor C267T polymorphism and response to antide... | BeFree | 15823158 | Detail |
| <0.001 | lingual-facial-buccal dyskinesia | Genetic association analysis of 5-HT(6) receptor gene polymorphism (267C/T) with... | BeFree | 12057822 | Detail |
| <0.001 | Hallucinations | In addition, the HTR6 T267C polymorphism has been linked to risperidone response... | BeFree | 15882132 | Detail |
| <0.001 | Tardive Dyskinesia | Genetic association analysis of 5-HT(6) receptor gene polymorphism (267C/T) with... | BeFree | 12057822 | Detail |
| <0.001 | dementia | In order to identify gene variants related to the serotonergic neurotransmitter ... | BeFree | 11725820 | Detail |
| 0.005 | Mental Depression | Association analysis of the 5-HT6 receptor polymorphism C267T with depression in... | BeFree | 11442897 | Detail |
| 0.003 | major depressive disorder | Association study of the 5-HT(6) receptor polymorphism (C267T) and symptomatolog... | BeFree | 11702016 | Detail |
| <0.001 | Delusions | In addition, the HTR6 T267C polymorphism has been linked to risperidone response... | BeFree | 15882132 | Detail |
| 0.003 | major depressive disorder | Association between the 5-HT6 receptor C267T polymorphism and response to antide... | BeFree | 15823158 | Detail |
| 0.003 | Mood Disorders | Association analysis of the 5-HT(6) receptor polymorphism (C267T) in mood disord... | BeFree | 10581475 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| In this study, we evaluated the association of seven serotonin signal transduction-linked single nuc... | DisGeNET | Detail |
| In this study, we evaluated the association of seven serotonin signal transduction-linked single nuc... | DisGeNET | Detail |
| In order to identify gene variants related to the serotonergic neurotransmitter system that possibly... | DisGeNET | Detail |
| In order to identify gene variants related to the serotonergic neurotransmitter system that possibly... | DisGeNET | Detail |
| In order to identify gene variants related to the serotonergic neurotransmitter system that possibly... | DisGeNET | Detail |
| Association between the 5-HT6 receptor C267T polymorphism and response to antidepressant treatment i... | DisGeNET | Detail |
| Genetic association analysis of 5-HT(6) receptor gene polymorphism (267C/T) with tardive dyskinesia. | DisGeNET | Detail |
| In addition, the HTR6 T267C polymorphism has been linked to risperidone response for positive sympto... | DisGeNET | Detail |
| Genetic association analysis of 5-HT(6) receptor gene polymorphism (267C/T) with tardive dyskinesia. | DisGeNET | Detail |
| In order to identify gene variants related to the serotonergic neurotransmitter system that possibly... | DisGeNET | Detail |
| Association analysis of the 5-HT6 receptor polymorphism C267T with depression in patients with Alzhe... | DisGeNET | Detail |
| Association study of the 5-HT(6) receptor polymorphism (C267T) and symptomatology and antidepressant... | DisGeNET | Detail |
| In addition, the HTR6 T267C polymorphism has been linked to risperidone response for positive sympto... | DisGeNET | Detail |
| Association between the 5-HT6 receptor C267T polymorphism and response to antidepressant treatment i... | DisGeNET | Detail |
| Association analysis of the 5-HT(6) receptor polymorphism (C267T) in mood disorders. | DisGeNET | Detail |
Overlapped Transcript Coordinates
| Gene | Transcript ID | Exon Number | Chromosome | Start | Stop | Type | Amino Mutation | Transcript Position | Links |
|---|
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- Genome
- hg38
- Position
- chr1:19,666,020-19,666,020
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1209
- Mean of sample read depth (HGVD)
- 214.52
- Standard deviation of sample read depth (HGVD)
- 99.83
- Number of reference allele (HGVD)
- 1694
- Number of alternative allele (HGVD)
- 724
- Allele Frequency (HGVD)
- 0.29942100909842845
- Gene Symbol (HGVD)
- HTR6
- ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- PASS
- Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- rs1805054
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.2993
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 5015
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16754
- East Asian Chromosome Counts (ExAC)
- 8532
- East Asian Allele Counts (ExAC)
- 2026
- East Asian Heterozygous Counts (ExAC)
- 1504
- East Asian Homozygous Counts (ExAC)
- 261
- East Asian Allele Frequency (ExAC)
- 0.23745897796530707
- Chromosome Counts in All Race (ExAC)
- 119954
- Allele Counts in All Race (ExAC)
- 18136
- Heterozygous Counts in All Race (ExAC)
- 15149
- Homozygous Counts in All Race (ExAC)
- 1493
- Allele Frequency in All Race (ExAC)
- 0.15119128999449788
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