HTR3D

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

Basic information

Region (hg38): 3:184031544-184039369

Links

ENSG00000186090 ∙ NCBI:200909 ∙ OMIM:610122 ∙ HGNC:24004 ∙ Uniprot:Q70Z44 ∙ 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 HTR3D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR3D 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				1		1
missense			32	8		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	33	9	0

Variants in HTR3D

This is a list of pathogenic ClinVar variants found in the HTR3D region.

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

Position	Type	Phenotype	Significance	ClinVar
3-184031760-C-T		not specified	Uncertain significance (Mar 07, 2024)
3-184031766-A-G		not specified	Likely benign (Apr 25, 2023)
3-184032841-A-G		not specified	Uncertain significance (Jan 22, 2024)
3-184032859-C-G		not specified	Uncertain significance (Jan 26, 2023)
3-184032870-C-G		not specified	Uncertain significance (Dec 01, 2022)
3-184032928-G-C		not specified	Uncertain significance (Oct 26, 2022)
3-184032933-G-C		not specified	Uncertain significance (May 04, 2023)
3-184033023-G-A		not specified	Uncertain significance (Nov 09, 2021)
3-184035174-C-G		not specified	Uncertain significance (May 03, 2023)
3-184035174-C-T		not specified	Uncertain significance (Mar 11, 2022)
3-184035988-C-T		not specified	Likely benign (Feb 28, 2023)
3-184035991-C-G		not specified	Uncertain significance (May 04, 2022)
3-184035998-A-G		not specified	Uncertain significance (Nov 18, 2023)
3-184036003-C-A		not specified	Uncertain significance (Apr 24, 2024)
3-184036014-G-A		not specified	Likely benign (Oct 02, 2023)
3-184036034-G-A		not specified	Uncertain significance (Feb 27, 2024)
3-184036043-A-G		not specified	Likely benign (Mar 19, 2024)
3-184036048-T-C		not specified	Uncertain significance (Jun 16, 2024)
3-184036054-A-G		not specified	Uncertain significance (Aug 02, 2023)
3-184036084-G-A		not specified	Likely benign (Aug 30, 2021)
3-184036093-G-A		not specified	Uncertain significance (Mar 28, 2023)
3-184036377-T-A		not specified	Uncertain significance (Jan 26, 2022)
3-184036382-C-A		not specified	Uncertain significance (Sep 09, 2021)
3-184036464-C-A		not specified	Uncertain significance (Feb 26, 2024)
3-184036751-G-A		not specified	Uncertain significance (Mar 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR3D	protein_coding	protein_coding	ENST00000382489	8	7826

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.02e-8	0.402	38094	27001	60650	125745	0.450

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.654	226	255	0.885	0.0000134	2926
Missense in Polyphen		36	51.25	0.70244		745
Synonymous	0.592	98	106	0.927	0.00000614	936
Loss of Function	0.771	13	16.4	0.794	7.78e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	1.10	1.09
Ashkenazi Jewish	0.578	0.578
East Asian	0.496	0.494
Finnish	0.318	0.316
European (Non-Finnish)	0.442	0.442
Middle Eastern	0.496	0.494
South Asian	0.452	0.450
Other	0.468	0.472

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: 0.305
• rvis_EVS: 2.51
• rvis_percentile_EVS: 98.66

Haploinsufficiency Scores

• pHI: 0.158
• 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: 0.111

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;protein binding;serotonin-gated cation-selective channel activity