HTR3E
protein-coding5-hydroxytryptamine receptor 3E, the group of 5-hydroxytryptamine receptors, ionotropic
Gene summary
This locus encodes a 5-hydroxytryptamine (serotonin) receptor subunit. The encoded protein, subunit E, may play a role in neurotransmission in myenteric neurons. Genes encoding subunits C, D and E form a cluster on chromosome 3. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Feb 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.9 kbGenCC 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 HTR3E variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001256613.2. 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 | 2 | 2 | ||||
| missense | 64 | 12 | 1 | 77 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 65 | 14 | 1 | 80 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001243542.1 | 9 | MANE Select | |
| Ensembl | ENSP00000401444.2 | 9 | MANE Select | |
| RefSeq | NP_001243543.1 | 7 | Standard | |
| RefSeq | NP_872395.2 | 8 | Standard |
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
- serotonin-gated cation-selective channel activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- neuron projection
- synapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000440596
- Coding exons
- 7
- Length
- 9932
- Individuals with no LoFs
- 125421
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 326
- Defined
- 125747
- p
- 0.00130
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.511 | 311 | 287 | 1.08 | 0.0000168 | 3149 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0089 | 0.0089 | notable |
| Finnish | 0.00018 | 0.00018 | rare |
| European (Non-Finnish) | 0.00012 | 0.00011 | rare |
| South Asian | 0.0044 | 0.0045 | notable |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- 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.;
Intolerance Scores
- LoFtool
- 0.390
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.76
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.262
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |