HTR1F
5-hydroxytryptamine receptor 1F, the group of 5-hydroxytryptamine receptors, G protein-coupled
Basic information
Region (hg38): 3:87792705-87993839
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR1F 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 | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 |
Variants in HTR1F
This is a list of pathogenic ClinVar variants found in the HTR1F region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-87990772-A-G | not specified | Uncertain significance (Aug 22, 2023) | ||
| 3-87990904-G-A | not specified | Uncertain significance (Nov 17, 2022) | ||
| 3-87991006-G-A | not specified | Uncertain significance (Nov 09, 2022) | ||
| 3-87991008-G-C | not specified | Uncertain significance (Aug 02, 2023) | ||
| 3-87991164-C-A | not specified | Uncertain significance (Jun 03, 2024) | ||
| 3-87991309-T-G | not specified | Uncertain significance (Oct 13, 2023) | ||
| 3-87991437-C-T | not specified | Uncertain significance (Aug 15, 2023) | ||
| 3-87991485-G-A | not specified | Uncertain significance (Jul 14, 2022) | ||
| 3-87991615-G-A | not specified | Uncertain significance (Apr 23, 2024) | ||
| 3-87991645-T-G | not specified | Uncertain significance (Jan 10, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HTR1F | protein_coding | protein_coding | ENST00000319595 | 1 | 3074 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00467 | 0.888 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.03 | 150 | 190 | 0.790 | 0.00000896 | 2389 |
| Missense in Polyphen | 69 | 87.594 | 0.78772 | 1114 | ||
| Synonymous | -1.70 | 89 | 70.8 | 1.26 | 0.00000333 | 739 |
| Loss of Function | 1.37 | 5 | 9.56 | 0.523 | 4.62e-7 | 139 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: G-protein coupled receptor for 5-hydroxytryptamine (serotonin). Also functions as a receptor for various alkaloids and psychoactive substances. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors, such as adenylate cyclase. Signaling inhibits adenylate cyclase activity. {ECO:0000269|PubMed:21422162, ECO:0000269|PubMed:8380639, ECO:0000269|PubMed:8384716}.;
- Pathway
- Serotonergic synapse - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Taste transduction - Homo sapiens (human);Selective Serotonin Reuptake Inhibitor Pathway, Pharmacodynamics;GPCRs, Other;GPCRs, Class A Rhodopsin-like;Monoamine GPCRs;Serotonin HTR1 Group and FOS Pathway;Signaling by GPCR;Signal Transduction;Serotonin receptors;Amine ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.122
Intolerance Scores
- loftool
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.64
Haploinsufficiency Scores
- pHI
- 0.449
- hipred
- N
- hipred_score
- 0.251
- ghis
- 0.412
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.450
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Htr1f
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;chemical synaptic transmission;G protein-coupled serotonin receptor signaling pathway
- Cellular component
- plasma membrane;integral component of plasma membrane;dendrite
- Molecular function
- G protein-coupled receptor activity;G protein-coupled serotonin receptor activity;neurotransmitter receptor activity;serotonin binding