HTR3D
protein-coding5-hydroxytryptamine receptor 3D, the group of 5-hydroxytryptamine receptors, ionotropic
Gene summary
The protein encoded this gene belongs to the ligand-gated ion channel receptor superfamily. This gene encodes subunit D of the type 3 receptor for 5-hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a mitogen and a hormone. This hormone has been linked to neuropsychiatric disorders, including anxiety, depression, and migraine. Serotonin receptors causes fast and depolarizing responses in neurons following activation. The genes encoding subunits C, D and E of this type 3 receptor form a cluster on chromosome 3. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~7.8 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 HTR3D variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001145143.1. 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 | 1 | ||||
| missense | 59 | 13 | 72 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 59 | 15 | 0 | 74 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001138615.1 | 8 | MANE Select | |
| Ensembl | ENSP00000405409.2 | 8 | MANE Select | |
| RefSeq | NP_001157118.1 | 8 | Standard | |
| RefSeq | NP_001397780.1 | 4 | 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
- protein binding
- 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
- ENST00000382489
- Coding exons
- 8
- Length
- 7826
- Individuals with no LoFs
- 38094
- Homozygous LoFs
- 27001
- Heterozygous LoFs
- 60650
- Defined
- 125745
- p
- 0.450
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.654 | 226 | 255 | 0.885 | 0.0000134 | 2926 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.67 | 0.66 | notable |
| Latino/Admixed American | 0.43 | 0.43 | notable |
| Ashkenazi Jewish | 0.58 | 0.58 | notable |
| East Asian | 0.50 | 0.49 | notable |
| Finnish | 0.32 | 0.32 | notable |
| European (Non-Finnish) | 0.44 | 0.44 | notable |
| South Asian | 0.45 | 0.45 | notable |
| Other | 0.47 | 0.47 | notable |
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
- 0.305
- RVIS EVS
- 2.51
- RVIS percentile EVS
- 98.66
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.111
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |