HTR3A

5-hydroxytryptamine receptor 3A, the group of 5-hydroxytryptamine receptors, ionotropic

Basic information

Region (hg38): 11:113975074-113990313

Previous symbols: [ "HTR3" ]

Links

ENSG00000166736 ∙ NCBI:3359 ∙ OMIM:182139 ∙ HGNC:5297 ∙ Uniprot:P46098 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HTR3A gene.

• Inborn genetic diseases (27 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR3A gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	3	6
missense			26	2	2	30
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	27	6	6

Variants in HTR3A

This is a list of pathogenic ClinVar variants found in the HTR3A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-113975319-G-T			Benign (Aug 20, 2018)
11-113977783-G-A		not specified	Uncertain significance (Feb 22, 2023)
11-113977835-C-A		not specified	Uncertain significance (Aug 15, 2023)
11-113977839-A-G		not specified	Uncertain significance (Jun 22, 2021)
11-113977870-G-T		not specified	Uncertain significance (Aug 10, 2021)
11-113977879-C-T		not specified	Uncertain significance (May 23, 2023)
11-113977919-C-A		not specified	Uncertain significance (Jul 17, 2023)
11-113979273-G-C		not specified	Uncertain significance (Jan 04, 2022)
11-113981321-C-T			Benign (Jun 11, 2018)
11-113981322-G-A			Likely benign (Jun 18, 2018)
11-113983121-G-A		not specified	Uncertain significance (Dec 16, 2022)
11-113983131-G-A		not specified	Uncertain significance (Jul 14, 2023)
11-113983153-C-T			Likely benign (Oct 01, 2022)
11-113983154-G-T		not specified	Uncertain significance (May 30, 2023)
11-113983164-G-A		not specified	Likely benign (Apr 05, 2023)
11-113983169-C-A		not specified	Uncertain significance (Oct 17, 2023)
11-113983175-G-A		not specified	Uncertain significance (Jul 09, 2021)
11-113983215-G-A		not specified	Uncertain significance (Jan 17, 2024)
11-113983263-T-G		not specified	Uncertain significance (Oct 05, 2022)
11-113986038-T-C		not specified	Uncertain significance (Aug 08, 2022)
11-113986116-C-T		not specified	Uncertain significance (May 04, 2023)
11-113986125-C-T			Likely benign (Aug 22, 2018)
11-113986150-AC-A			Uncertain significance (Jan 11, 2024)
11-113986159-C-G		not specified	Uncertain significance (Nov 14, 2023)
11-113986531-G-A		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR3A	protein_coding	protein_coding	ENST00000355556	8	15433

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.75e-10	0.385	125497	2	249	125748	0.000999

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.17	350	294	1.19	0.0000187	3334
Missense in Polyphen		120	113.43	1.0579		1335
Synonymous	-0.533	136	128	1.06	0.00000860	1075
Loss of Function	1.03	18	23.4	0.769	0.00000129	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0122	0.0122
Ashkenazi Jewish	0.00	0.00
East Asian	0.000924	0.000925
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000924	0.000925
South Asian	0.000196	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This is one of the several different receptors for 5- hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. This receptor is a ligand-gated ion channel, which when activated causes fast, depolarizing responses in neurons. It is a cation-specific, but otherwise relatively nonselective, ion channel. {ECO:0000269|PubMed:12867984, ECO:0000269|PubMed:9950429}.
• Pathway: Serotonergic synapse - Homo sapiens (human);Taste transduction - Homo sapiens (human);Selective Serotonin Reuptake Inhibitor Pathway, Pharmacodynamics;Selective serotonin reuptake inhibitors lead to several adverse outcomes;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.241

Intolerance Scores

• loftool: 0.202
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.86

Haploinsufficiency Scores

• pHI: 0.271
• hipred: N
• hipred_score: 0.251
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.264

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Htr3a
• Phenotype: homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Gene ontology

• Biological process: signal transduction;serotonin receptor signaling pathway;chemical synaptic transmission;positive regulation of ion transmembrane transporter activity;ion transmembrane transport;response to cocaine;regulation of membrane potential;response to ethanol;nervous system process;cellular response to growth factor stimulus
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane;cell junction;axon;cleavage furrow;neuron projection;neuronal cell body;synapse;glutamatergic synapse;integral component of postsynaptic membrane;integral component of presynaptic membrane;serotonin-activated cation-selective channel complex
• Molecular function: transmembrane signaling receptor activity;extracellular ligand-gated ion channel activity;protein binding;serotonin-gated cation-selective channel activity;serotonin binding