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

ENSG00000102468NCBI:3356OMIM:182135HGNC:5293Uniprot:P28223AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Major depressive disorder, response to citalopram therapy in; Clozapine, response toADPharmacogenomicVariants may relate to the efficacy of medications such as Citalopram and clozapineGeneral9491814; 12563180; 16642436

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HTR2A gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
2
clinvar
9
missense
22
clinvar
1
clinvar
23
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 0 0 23 8 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
HTR2Aprotein_codingprotein_codingENST00000378688 365485
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.5110.4881257370111257480.0000437
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.751772560.6920.00001453083
Missense in Polyphen54115.730.466611386
Synonymous-0.1471091071.020.00000670935
Loss of Function2.86314.90.2017.07e-7189

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009050.0000904
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00004400.0000439
Middle Eastern0.000.00
South Asian0.00009840.0000980
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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