chr13:47409034:G>A Detail (hg19) (HTR2A)

Information

Genome

Assembly Position
hg19 chr13:47,409,034-47,409,034
hg38 chr13:46,834,899-46,834,899 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001165947.2:c.865C>T NP_001159419.1:p.His289Tyr
NM_000621.4:c.1354C>T NP_000612.1:p.His452Tyr
Ensemble ENST00000543956.5:c.865C>T ENST00000543956.5:p.His289Tyr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 182135 OMIM
HGNC 5293 HGNC
Ensembl ENSG00000102468 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv48540412 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.008 rheumatoid arthritis Patients with established RA (n=379) were genotyped for two single-nucleotide po... BeFree 23254357 Detail
0.011 Unipolar Depression Accordingly, two single nucleotide polymorphisms of the HTR2A gene (rs6314 ie Hi... BeFree 24801750 Detail
0.155 major depressive disorder Accordingly, two single nucleotide polymorphisms of the HTR2A gene (rs6314 ie Hi... BeFree 24801750 Detail
0.009 obesity Polymorphisms in the monoamine oxidase A (MAOA-LPR) and serotonin receptor 2A ge... BeFree 23544600 Detail
0.341 schizophrenia Our results suggest that HTR2A rs6314 affects 5-HT2AR expression and functionall... BeFree 23842608 Detail
0.134 obesity Polymorphisms in the monoamine oxidase A (MAOA-LPR) and serotonin receptor 2A ge... BeFree 23544600 Detail
Annotation

Annotations

DescrptionSourceLinks
Patients with established RA (n=379) were genotyped for two single-nucleotide polymorphisms (SNPs) i... DisGeNET Detail
Accordingly, two single nucleotide polymorphisms of the HTR2A gene (rs6314 ie His452Tyr and rs6313 i... DisGeNET Detail
Accordingly, two single nucleotide polymorphisms of the HTR2A gene (rs6314 ie His452Tyr and rs6313 i... DisGeNET Detail
Polymorphisms in the monoamine oxidase A (MAOA-LPR) and serotonin receptor 2A genes (rs6314) moderat... DisGeNET Detail
Our results suggest that HTR2A rs6314 affects 5-HT2AR expression and functionally contributes to gen... DisGeNET Detail
Polymorphisms in the monoamine oxidase A (MAOA-LPR) and serotonin receptor 2A genes (rs6314) moderat... 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
hg19
Position
chr13:47,409,034-47,409,034
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
150.60
Standard deviation of sample read depth (HGVD)
64.56
Number of reference allele (HGVD)
2418
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.264462809917355E-4
Gene Symbol (HGVD)
HTR2A
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))
rs6314
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0002
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
8
East Asian Heterozygous Counts (ExAC)
8
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
9.248554913294797E-4
Chromosome Counts in All Race (ExAC)
121246
Allele Counts in All Race (ExAC)
9574
Heterozygous Counts in All Race (ExAC)
8716
Homozygous Counts in All Race (ExAC)
429
Allele Frequency in All Race (ExAC)
0.07896342972139286
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