HRH2
histamine receptor H2, the group of Histamine receptors
Basic information
Region (hg38): 5:175658030-175710756
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 HRH2 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 2 | 0 |
Variants in HRH2
This is a list of pathogenic ClinVar variants found in the HRH2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-175683481-A-G | Myoepithelial tumor | Uncertain significance (Nov 01, 2022) | ||
| 5-175683642-A-G | not specified | Likely benign (Dec 16, 2022) | ||
| 5-175683912-A-G | not specified | Uncertain significance (Dec 27, 2023) | ||
| 5-175684159-A-G | not specified | Likely benign (Nov 08, 2022) | ||
| 5-175684161-C-T | not specified | Uncertain significance (Aug 04, 2023) | ||
| 5-175684183-T-C | not specified | Uncertain significance (Jan 10, 2023) | ||
| 5-175684269-A-G | not specified | Uncertain significance (Jan 02, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HRH2 | protein_coding | protein_coding | ENST00000377291 | 2 | 28213 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.122 | 0.856 | 125729 | 0 | 3 | 125732 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.53 | 116 | 222 | 0.522 | 0.0000144 | 2571 |
| Missense in Polyphen | 25 | 95.162 | 0.26271 | 1078 | ||
| Synonymous | -0.0468 | 100 | 99.4 | 1.01 | 0.00000656 | 864 |
| Loss of Function | 1.97 | 3 | 9.56 | 0.314 | 5.06e-7 | 104 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: The H2 subclass of histamine receptors mediates gastric acid secretion. Also appears to regulate gastrointestinal motility and intestinal secretion. Possible role in regulating cell growth and differentiation. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase and, through a separate G protein-dependent mechanism, the phosphoinositide/protein kinase (PKC) signaling pathway (By similarity). {ECO:0000250}.;
- Pathway
- Gastric acid secretion - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Proton Pump Inhibitor Pathway, Pharmacodynamics;Cimetidine Metabolism Pathway;Pantoprazole Action Pathway;Rabeprazole Action Pathway;Esomeprazole Action Pathway;Omeprazole Action Pathway;Lansoprazole Action Pathway;Gastric Acid Production;Nizatidine Action Pathway;Cimetidine Action Pathway;Famotidine Action Pathway;Ranitidine Action Pathway;Intracellular Signalling Through Histamine H2 Receptor and Histamine;Betazole Action Pathway;Roxatidine acetate Action Pathway;Metiamide Action Pathway;Pirenzepine Action Pathway;Secretion of Hydrochloric Acid in Parietal Cells;GPCRs, Class A Rhodopsin-like;Monoamine GPCRs;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Histamine receptors;Amine ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.150
Intolerance Scores
- loftool
- 0.301
- rvis_EVS
- -0.52
- rvis_percentile_EVS
- 21.2
Haploinsufficiency Scores
- pHI
- 0.132
- hipred
- Y
- hipred_score
- 0.806
- ghis
- 0.639
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.550
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hrh2
- Phenotype
- homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); digestive/alimentary phenotype;
Gene ontology
- Biological process
- histamine-induced gastric acid secretion;gastrin-induced gastric acid secretion;epithelial cell morphogenesis;immune response;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;chemical synaptic transmission;memory;visual learning;positive regulation of vasoconstriction;regulation of synaptic plasticity;digestive tract development;gland development;G protein-coupled serotonin receptor signaling pathway;toxin transport
- Cellular component
- plasma membrane;integral component of plasma membrane;dendrite
- Molecular function
- G protein-coupled receptor activity;histamine receptor activity;G protein-coupled serotonin receptor activity;neurotransmitter receptor activity