HTR2A
5-hydroxytryptamine receptor 2A, the group of 5-hydroxytryptamine receptors, G protein-coupled
Basic information
Region (hg38): 13:46831546-46897076
Previous symbols: [ "HTR2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Major depressive disorder, response to citalopram therapy in; Clozapine, response to | AD | Pharmacogenomic | Variants may relate to the efficacy of medications such as Citalopram and clozapine | General | 9491814; 12563180; 16642436 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (23 variants)
- not_provided (10 variants)
- HTR2A-related_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR2A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000621.5. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 9 | |||||
| missense | 22 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 23 | 8 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HTR2A | protein_coding | protein_coding | ENST00000378688 | 3 | 65485 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.511 | 0.488 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.75 | 177 | 256 | 0.692 | 0.0000145 | 3083 |
| Missense in Polyphen | 54 | 115.73 | 0.46661 | 1386 | ||
| Synonymous | -0.147 | 109 | 107 | 1.02 | 0.00000670 | 935 |
| Loss of Function | 2.86 | 3 | 14.9 | 0.201 | 7.07e-7 | 189 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000905 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000440 | 0.0000439 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000984 | 0.0000980 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: G-protein coupled receptor for 5-hydroxytryptamine (serotonin) (PubMed:1330647, PubMed:18703043, PubMed:19057895). Also functions as a receptor for various drugs and psychoactive substances, including mescaline, psilocybin, 1-(2,5-dimethoxy-4- iodophenyl)-2-aminopropane (DOI) and lysergic acid diethylamide (LSD) (PubMed:28129538). Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors (PubMed:28129538). Beta-arrestin family members inhibit signaling via G proteins and mediate activation of alternative signaling pathways (PubMed:28129538). Signaling activates phospholipase C and a phosphatidylinositol-calcium second messenger system that modulates the activity of phosphatidylinositol 3-kinase and promotes the release of Ca(2+) ions from intracellular stores (PubMed:18703043, PubMed:28129538). Affects neural activity, perception, cognition and mood (PubMed:18297054). Plays a role in the regulation of behavior, including responses to anxiogenic situations and psychoactive substances. Plays a role in intestinal smooth muscle contraction, and may play a role in arterial vasoconstriction. {ECO:0000269|PubMed:1330647, ECO:0000269|PubMed:18297054, ECO:0000269|PubMed:18703043, ECO:0000269|PubMed:19057895, ECO:0000269|PubMed:21645528, ECO:0000269|PubMed:22300836, ECO:0000269|PubMed:28129538}.;
- Pathway
- Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Gap junction - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Selective Serotonin Reuptake Inhibitor Pathway, Pharmacodynamics;GPCRs, Other;Serotonin and anxiety;Serotonin and anxiety-related events;Selective serotonin reuptake inhibitors lead to several adverse outcomes;GPCRs, Class A Rhodopsin-like;Monoamine GPCRs;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Serotonin Receptor 2 and ELK-SRF-GATA4 signaling;Serotonin Receptor 2 and STAT3 Signaling;Signaling by GPCR;Signal Transduction;Serotonin receptors;Amine ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.342
Intolerance Scores
- loftool
- 0.186
- rvis_EVS
- 0.44
- rvis_percentile_EVS
- 77.8
Haploinsufficiency Scores
- pHI
- 0.414
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.413
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.621
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Htr2a
- Phenotype
- muscle phenotype; endocrine/exocrine gland phenotype; digestive/alimentary phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- htr2ab
- Affected structure
- commissure of the tract of the commissure of the caudal tuberculum
- Phenotype tag
- abnormal
- Phenotype quality
- decreased process quality
Gene ontology
- Biological process
- temperature homeostasis;cellular calcium ion homeostasis;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;phospholipase C-activating G protein-coupled receptor signaling pathway;activation of phospholipase C activity;phospholipase C-activating serotonin receptor signaling pathway;serotonin receptor signaling pathway;chemical synaptic transmission;aging;memory;cell death;positive regulation of cell population proliferation;positive regulation of phosphatidylinositol biosynthetic process;regulation of dopamine secretion;phosphatidylinositol 3-kinase signaling;artery smooth muscle contraction;urinary bladder smooth muscle contraction;sleep;response to drug;negative regulation of potassium ion transport;positive regulation of MAP kinase activity;protein localization to cytoskeleton;positive regulation of fat cell differentiation;positive regulation of glycolytic process;positive regulation of vasoconstriction;viral entry into host cell;behavioral response to cocaine;positive regulation of peptidyl-tyrosine phosphorylation;detection of temperature stimulus involved in sensory perception of pain;detection of mechanical stimulus involved in sensory perception of pain;release of sequestered calcium ion into cytosol;negative regulation of synaptic transmission, glutamatergic;positive regulation of ERK1 and ERK2 cascade;regulation of synaptic vesicle exocytosis
- Cellular component
- cytosol;plasma membrane;integral component of plasma membrane;caveola;axon;dendrite;cytoplasmic vesicle;neuronal cell body;dendritic shaft;cell body fiber;glutamatergic synapse;integral component of postsynaptic membrane;integral component of presynaptic membrane
- Molecular function
- virus receptor activity;G-protein alpha-subunit binding;G protein-coupled receptor activity;G protein-coupled serotonin receptor activity;drug binding;neurotransmitter receptor activity;protein-containing complex binding;serotonin binding;1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding