HTR3B

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

Basic information

Region (hg38): 11:113904795-113949079

Links

ENSG00000149305 ∙ NCBI:9177 ∙ OMIM:604654 ∙ HGNC:5298 ∙ Uniprot:O95264 ∙ 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 HTR3B gene.

• Inborn genetic diseases (12 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR3B 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						0
missense			12	1	2	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	12	1	2

Variants in HTR3B

This is a list of pathogenic ClinVar variants found in the HTR3B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-113904964-G-A		not specified	Uncertain significance (Dec 14, 2023)
11-113909348-A-G		not specified	Uncertain significance (Jan 18, 2022)
11-113909368-A-T		not specified	Likely benign (Dec 22, 2023)
11-113909402-A-G		not specified	Uncertain significance (Dec 27, 2023)
11-113909409-C-T		not specified	Uncertain significance (Mar 07, 2023)
11-113931385-A-T		not specified	Uncertain significance (Jun 29, 2022)
11-113931845-C-T		not specified	Uncertain significance (Dec 16, 2023)
11-113932286-T-C			Benign (Feb 02, 2018)
11-113932327-A-G		not specified	Uncertain significance (Jun 23, 2023)
11-113932360-A-G		not specified	Uncertain significance (Dec 17, 2023)
11-113932365-A-G		not specified	Uncertain significance (Feb 26, 2024)
11-113932387-G-A		not specified	Uncertain significance (Sep 28, 2021)
11-113933080-A-G		not specified	Uncertain significance (Dec 21, 2023)
11-113942998-A-T		not specified	Uncertain significance (Feb 07, 2023)
11-113943015-G-A		not specified	Uncertain significance (Jan 26, 2022)
11-113943054-G-T		not specified	Uncertain significance (Jun 28, 2023)
11-113943087-C-G		not specified	Uncertain significance (Sep 20, 2023)
11-113943097-T-G			Benign (Dec 31, 2019)
11-113943148-T-G		not specified	Uncertain significance (May 16, 2022)
11-113944632-T-G			Likely benign (Jun 15, 2018)
11-113944677-C-G		not specified	Uncertain significance (Jan 16, 2024)
11-113944725-G-A			Benign (Mar 29, 2018)
11-113945919-G-A		not specified	Uncertain significance (Aug 04, 2022)
11-113946025-G-T		not specified	Uncertain significance (Apr 13, 2022)
11-113946042-C-T		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR3B	protein_coding	protein_coding	ENST00000260191	9	41889

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.48e-7	0.911	125660	0	87	125747	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0252	242	243	0.995	0.0000126	2885
Missense in Polyphen		83	84.355	0.98394		1134
Synonymous	0.757	88	97.5	0.902	0.00000519	852
Loss of Function	1.72	14	22.9	0.612	0.00000113	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00115	0.00115
Ashkenazi Jewish	0.00139	0.00139
East Asian	0.000490	0.000489
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.000490	0.000489
South Asian	0.000458	0.000457
Other	0.000825	0.000815

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. It is a cation-specific, but otherwise relatively nonselective, ion channel. {ECO:0000269|PubMed:12867984}.
• Pathway: Serotonergic synapse - Homo sapiens (human);Taste transduction - Homo sapiens (human);Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.0916

Intolerance Scores

• loftool: 0.416
• rvis_EVS: 1
• rvis_percentile_EVS: 90.65

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.144
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.165

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Htr3b
• Phenotype: growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Biological process: signal transduction;serotonin receptor signaling pathway;chemical synaptic transmission;ion transmembrane transport;regulation of membrane potential;nervous system process
• Cellular component: plasma membrane;integral component of plasma membrane;cell surface;neuron projection;synapse;postsynaptic membrane;serotonin-activated cation-selective channel complex
• Molecular function: transmembrane signaling receptor activity;extracellular ligand-gated ion channel activity;serotonin-gated cation-selective channel activity