HTR3B

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

Basic information

Region (hg38): 11:113904796-113949079

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.

not_specified (63 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. These statistics are base on transcript: NM_000006028.5. 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						0
missense			61 clinvar	3 clinvar	2 clinvar	66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	61	3	2

Loading clinvar variants...

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