HTR2B

5-hydroxytryptamine receptor 2B, the group of 5-hydroxytryptamine receptors, G protein-coupled

Basic information

Region (hg38): 2:231108229-231125042

Links

ENSG00000135914 ∙ NCBI:3357 ∙ OMIM:601122 ∙ HGNC:5294 ∙ Uniprot:P41595 ∙ 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 HTR2B gene.

• Inborn genetic diseases (16 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR2B 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					2	2
missense			16	1	4	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	6

Variants in HTR2B

This is a list of pathogenic ClinVar variants found in the HTR2B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-231108553-T-G		not specified	Uncertain significance (Jun 02, 2023)
2-231108575-G-T		not specified	Uncertain significance (Jul 06, 2021)
2-231108649-G-A			Benign (Jun 18, 2018)
2-231108702-T-C			Benign (Jul 15, 2018)
2-231108710-C-T		not specified	Likely benign (Dec 07, 2023)
2-231108720-T-A		not specified	Uncertain significance (Oct 06, 2023)
2-231108732-G-A		not specified	Likely benign (Jun 29, 2023)
2-231108978-C-A		not specified	Uncertain significance (Oct 17, 2023)
2-231109009-G-C		not specified	Uncertain significance (Feb 01, 2023)
2-231109038-C-T		not specified	Uncertain significance (Jul 20, 2021)
2-231109103-G-A		not specified	Uncertain significance (Dec 13, 2022)
2-231109129-C-T			Benign (Jul 11, 2018)
2-231109148-T-C		not specified	Uncertain significance (Nov 07, 2022)
2-231109197-G-A		not specified	Uncertain significance (Nov 30, 2022)
2-231109227-T-A		Bardet-Biedl syndrome	Uncertain significance (-)
2-231109341-C-A			Benign (Jul 15, 2018)
2-231113777-G-A		not specified	Uncertain significance (May 18, 2022)
2-231113819-T-C			Uncertain significance (Apr 11, 2018)
2-231113824-C-T		not specified	Uncertain significance (Dec 20, 2023)
2-231113869-A-G		not specified	Uncertain significance (Jan 02, 2024)
2-231113914-A-G		not specified	Uncertain significance (Jun 29, 2023)
2-231113918-G-T		not specified	Uncertain significance (Jun 22, 2021)
2-231123440-G-T		not specified	Uncertain significance (Jun 26, 2023)
2-231123457-A-G		not specified	Uncertain significance (May 26, 2022)
2-231123613-C-T			Benign (Jun 18, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR2B	protein_coding	protein_coding	ENST00000258400	3	16889

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.69e-10	0.152	125182	2	564	125748	0.00225

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.134	258	252	1.02	0.0000137	3113
Missense in Polyphen		91	92.718	0.98147		1199
Synonymous	-0.767	101	91.7	1.10	0.00000491	992
Loss of Function	0.480	16	18.2	0.878	0.00000119	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00159	0.00153
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.00103	0.00103
Finnish	0.0160	0.0160
European (Non-Finnish)	0.000635	0.000633
Middle Eastern	0.00103	0.00103
South Asian	0.00229	0.00229
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: G-protein coupled receptor for 5-hydroxytryptamine (serotonin) (PubMed:8143856, PubMed:7926008, PubMed:8078486, PubMed:8882600, PubMed:18703043, PubMed:23519210). Also functions as a receptor for various ergot alkaloid derivatives and psychoactive substances (PubMed:8143856, PubMed:7926008, PubMed:8078486, PubMed:12970106, PubMed:18703043, PubMed:23519210, PubMed:23519215, PubMed:24357322, 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:8143856, PubMed:8078486, PubMed:8882600, PubMed:23519215, PubMed:28129538). Beta-arrestin family members inhibit signaling via G proteins and mediate activation of alternative signaling pathways (PubMed:23519215, PubMed:28129538). Signaling activates a phosphatidylinositol- calcium second messenger system that modulates the activity of phosphatidylinositol 3-kinase and down-stream signaling cascades and promotes the release of Ca(2+) ions from intracellular stores (PubMed:8143856, PubMed:8078486, PubMed:8882600, PubMed:18703043, PubMed:23519215, PubMed:28129538). Plays a role in the regulation of dopamine and 5-hydroxytryptamine release, 5-hydroxytryptamine uptake and in the regulation of extracellular dopamine and 5- hydroxytryptamine levels, and thereby affects neural activity. May play a role in the perception of pain (By similarity). Plays a role in the regulation of behavior, including impulsive behavior (PubMed:21179162). Required for normal proliferation of embryonic cardiac myocytes and normal heart development. Protects cardiomyocytes against apoptosis. Plays a role in the adaptation of pulmonary arteries to chronic hypoxia. Plays a role in vasoconstriction. Required for normal osteoblast function and proliferation, and for maintaining normal bone density. Required for normal proliferation of the interstitial cells of Cajal in the intestine (By similarity). {ECO:0000250|UniProtKB:P30994, ECO:0000250|UniProtKB:Q02152, ECO:0000269|PubMed:12970106, ECO:0000269|PubMed:18703043, ECO:0000269|PubMed:21179162, ECO:0000269|PubMed:23519210, ECO:0000269|PubMed:23519215, ECO:0000269|PubMed:24357322, ECO:0000269|PubMed:28129538, ECO:0000269|PubMed:7926008, ECO:0000269|PubMed:8078486, ECO:0000269|PubMed:8143856, ECO:0000269|PubMed:8882600}.
• 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);GPCRs, Class A Rhodopsin-like;Monoamine GPCRs;Serotonin Receptor 2 and ELK-SRF-GATA4 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: 0.136

Intolerance Scores

• loftool: 0.915
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.396
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Htr2b
• Phenotype: cellular phenotype; muscle phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); normal phenotype; reproductive system phenotype

Gene ontology

• Biological process: neural crest cell migration;positive regulation of cytokine production;positive regulation of endothelial cell proliferation;G protein-coupled receptor internalization;heart morphogenesis;cardiac muscle hypertrophy;cellular calcium ion homeostasis;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;activation of phospholipase C activity;protein kinase C-activating G protein-coupled receptor signaling pathway;serotonin receptor signaling pathway;chemical synaptic transmission;behavior;positive regulation of cell population proliferation;negative regulation of autophagy;positive regulation of phosphatidylinositol biosynthetic process;neural crest cell differentiation;phosphatidylinositol 3-kinase signaling;intestine smooth muscle contraction;phosphorylation;calcium-mediated signaling;cGMP-mediated signaling;vasoconstriction;response to drug;negative regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of MAP kinase activity;positive regulation of GTPase activity;embryonic morphogenesis;positive regulation of cytokine secretion;regulation of behavior;positive regulation of nitric-oxide synthase activity;release of sequestered calcium ion into cytosol;positive regulation of cell division;negative regulation of cell death;ERK1 and ERK2 cascade;positive regulation of ERK1 and ERK2 cascade;protein kinase C signaling;cellular response to temperature stimulus;G protein-coupled serotonin receptor signaling pathway
• Cellular component: nucleoplasm;cytoplasm;plasma membrane;integral component of plasma membrane;cell junction;dendrite;synapse
• Molecular function: G-protein alpha-subunit binding;G protein-coupled receptor activity;G protein-coupled serotonin receptor activity;GTPase activator activity;drug binding;neurotransmitter receptor activity;serotonin binding