HTR3C

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

Basic information

Region (hg38): 3:184053047-184060673

Links

ENSG00000178084 ∙ NCBI:170572 ∙ OMIM:610121 ∙ HGNC:24003 ∙ Uniprot:Q8WXA8 ∙ 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 HTR3C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR3C 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	2	3
missense			14	6	2	22
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	7	5

Variants in HTR3C

This is a list of pathogenic ClinVar variants found in the HTR3C region.

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

Position	Type	Phenotype	Significance	ClinVar
3-184054731-C-T			Benign (Jul 02, 2018)
3-184054762-C-A		not specified	Uncertain significance (Apr 13, 2022)
3-184054769-G-C		not specified	Uncertain significance (Nov 22, 2022)
3-184054776-C-A		not specified	Uncertain significance (Dec 13, 2023)
3-184054847-G-A		not specified	Likely benign (Nov 14, 2023)
3-184055334-C-T		not specified	Uncertain significance (Feb 06, 2023)
3-184056883-T-C		not specified	Uncertain significance (Sep 30, 2024)
3-184056892-C-T		not specified	Uncertain significance (Nov 19, 2022)
3-184056922-G-A		not specified	Uncertain significance (Sep 11, 2024)
3-184056925-A-G			Likely benign (Aug 21, 2018)
3-184056961-C-A			Benign (Jul 31, 2018)
3-184056965-C-T			Benign (Jul 31, 2018)
3-184056988-A-G		not specified	Uncertain significance (Oct 12, 2021)
3-184057026-A-G		not specified	Uncertain significance (Nov 17, 2023)
3-184057041-A-G		not specified	Uncertain significance (Jul 02, 2024)
3-184058483-C-T		not specified	Uncertain significance (Apr 19, 2023)
3-184058484-G-A		not specified	Likely benign (Dec 27, 2023)
3-184059440-C-T		not specified	Uncertain significance (Jun 02, 2024)
3-184059448-C-T		not specified	Uncertain significance (May 30, 2024)
3-184059457-A-G		not specified	Uncertain significance (Jan 30, 2024)
3-184059509-A-G		not specified	Uncertain significance (Sep 08, 2024)
3-184059540-C-T			Likely benign (Aug 01, 2018)
3-184059548-G-A		not specified	Likely benign (May 04, 2023)
3-184059557-T-G		not specified	Uncertain significance (Oct 05, 2021)
3-184059634-C-T		not specified	Likely benign (Oct 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR3C	protein_coding	protein_coding	ENST00000318351	9	7625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.56e-10	0.148	125598	1	148	125747	0.000593

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.276	261	249	1.05	0.0000132	2935
Missense in Polyphen		46	45.236	1.0169		666
Synonymous	-0.237	105	102	1.03	0.00000571	892
Loss of Function	0.468	16	18.2	0.881	9.38e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00256	0.00255
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.00246	0.00242
Other	0.00	0.00

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)

Recessive Scores

• pRec: 0.0711

Intolerance Scores

• loftool: 0.487
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.54

Haploinsufficiency Scores

• pHI: 0.128
• 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: 0.265

Gene Damage Prediction

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

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