HTR3E

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

Basic information

Region (hg38): 3:184097064-184106995

Links

ENSG00000186038 ∙ NCBI:285242 ∙ OMIM:610123 ∙ HGNC:24005 ∙ Uniprot:A5X5Y0 ∙ 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 HTR3E gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR3E 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			35	6	2	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	6	2

Variants in HTR3E

This is a list of pathogenic ClinVar variants found in the HTR3E region.

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

Position	Type	Phenotype	Significance	ClinVar
3-184100385-A-G		not specified	Uncertain significance (Feb 27, 2024)
3-184100595-A-G		not specified	Uncertain significance (Dec 12, 2023)
3-184100601-G-C		not specified	Uncertain significance (Mar 27, 2023)
3-184100608-C-T		not specified	Uncertain significance (Aug 20, 2024)
3-184100628-G-A			Benign (Feb 18, 2020)
3-184104205-C-A		not specified	Likely benign (Apr 08, 2024)
3-184104206-T-C		not specified	Uncertain significance (Oct 27, 2023)
3-184104234-C-T		not specified	Uncertain significance (Aug 01, 2022)
3-184104243-G-A		not specified	Uncertain significance (Jan 09, 2024)
3-184104249-C-T		not specified	Uncertain significance (Feb 07, 2023)
3-184104260-C-G		not specified	Uncertain significance (Jan 12, 2024)
3-184104270-C-A		not specified	Uncertain significance (Mar 20, 2023)
3-184104798-A-G		not specified	Uncertain significance (Aug 02, 2021)
3-184104812-G-A		not specified	Uncertain significance (May 13, 2024)
3-184104827-G-A		not specified	Likely benign (Nov 15, 2024)
3-184104870-T-C		not specified	Uncertain significance (Aug 17, 2022)
3-184105280-G-C		not specified	Uncertain significance (Feb 10, 2022)
3-184105289-G-A		not specified	Uncertain significance (Dec 21, 2023)
3-184105317-G-A		not specified	Likely benign (Sep 07, 2022)
3-184105324-G-A			Likely benign (Mar 31, 2018)
3-184105773-C-G		not specified	Uncertain significance (Jul 26, 2022)
3-184105789-C-T		not specified	Uncertain significance (Dec 08, 2023)
3-184105793-A-G		not specified	Uncertain significance (Jun 06, 2023)
3-184105803-C-A		not specified	Uncertain significance (Apr 17, 2023)
3-184105838-A-G		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR3E	protein_coding	protein_coding	ENST00000440596	7	9932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.23e-10	0.0559	125421	0	326	125747	0.00130

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.511	311	287	1.08	0.0000168	3149
Missense in Polyphen		62	55.263	1.1219		761
Synonymous	0.867	109	121	0.900	0.00000777	976
Loss of Function	-0.183	14	13.3	1.05	5.60e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.00886	0.00890
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.00886	0.00890
South Asian	0.00444	0.00445
Other	0.000490	0.000489

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.
• Pathway: Serotonergic synapse - Homo sapiens (human);Taste transduction - Homo sapiens (human);Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Intolerance Scores

• loftool: 0.390
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.76

Haploinsufficiency Scores

• pHI: 0.0848
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.262

Gene Damage Prediction

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

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;neuron projection;synapse
• Molecular function: transmembrane signaling receptor activity;extracellular ligand-gated ion channel activity;serotonin-gated cation-selective channel activity