HTR3C

protein-coding

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

Gene summary

The product of this gene belongs to the ligand-gated ion channel receptor superfamily. This gene encodes subunit C of the type 3 receptor for 5-hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. This receptor causes fast, depolarizing responses in neurons after activation. Genes encoding subunits C, D and E form a cluster on chromosome 3. [provided by RefSeq, Jul 2008]

MANE transcript

NM_130770.3

Inheritance

—

ClinVar variants

U:57B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr3:184,053,047-184,060,673

External References & Databases

Ensembl (ENSG00000178084)

Transcript & Mutation Effects

hg38 • Region Span ~7.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HTR3C variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_130770.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	2 clinvar	3
missense			57 clinvar	10 clinvar	2 clinvar	69
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	11	5	73

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_130770.3	RefSeq	NP_570126.2	9	MANE Select
ENST00000318351.2	Ensembl	ENSP00000322617.1	9	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Serotonergic synapse - Homo sapiens (human)
Taste transduction - Homo sapiens (human)
Neuronal System
Neurotransmitter receptors and postsynaptic signal transmission
Transmission across Chemical Synapses

Biological Process

signal transduction
serotonin receptor signaling pathway
chemical synaptic transmission
ion transmembrane transport
regulation of membrane potential

Molecular Function

transmembrane signaling receptor activity
extracellular ligand-gated ion channel activity
protein binding
serotonin-gated cation-selective channel activity

Cellular Component

plasma membrane
integral component of plasma membrane
neuron projection
synapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000318351
Coding exons: 9
Length: 7625
Individuals with no LoFs: 125598
Homozygous LoFs: 1
Heterozygous LoFs: 148
Defined: 125747
p: 0.000593

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.276	261	249	1.05	0.0000132	2935
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0019	0.0019	notable
Latino/Admixed American	0.00064	0.00064	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.0025	0.0024	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.0711

Intolerance Scores

LoFtool: 0.487
RVIS EVS: 0.91
RVIS percentile EVS: 89.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.265

Gene Damage Prediction

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