HRH1

histamine receptor H1, the group of Histamine receptors

Basic information

Region (hg38): 3:11137092-11263557

Links

ENSG00000196639 ∙ NCBI:3269 ∙ OMIM:600167 ∙ HGNC:5182 ∙ Uniprot:P35367 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HRH1 gene.

• Inborn genetic diseases (6 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HRH1 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		4	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	4

Variants in HRH1

This is a list of pathogenic ClinVar variants found in the HRH1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-11259079-G-A			Benign (Jul 06, 2018)
3-11259094-G-C			Benign (Jul 07, 2018)
3-11259102-T-C		not specified	Uncertain significance (Nov 07, 2023)
3-11259200-G-A		not specified	Uncertain significance (Jan 31, 2023)
3-11259251-G-A		not specified	Uncertain significance (Apr 25, 2023)
3-11259279-T-C		not specified	Uncertain significance (Feb 05, 2024)
3-11259618-C-G		not specified	Uncertain significance (Feb 03, 2022)
3-11259707-C-T		not specified	Uncertain significance (Feb 22, 2023)
3-11260014-G-A			Benign (Aug 08, 2018)
3-11260082-G-C			Benign (Jun 20, 2018)
3-11260104-A-G		not specified	Uncertain significance (Mar 21, 2023)
3-11260374-A-G		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HRH1	protein_coding	protein_coding	ENST00000397056	1	126465

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000186	0.693	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.813	238	276	0.862	0.0000158	3206
Missense in Polyphen		76	101.64	0.74776		1207
Synonymous	-0.610	118	110	1.07	0.00000624	966
Loss of Function	1.11	11	15.8	0.698	9.37e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000619	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In peripheral tissues, the H1 subclass of histamine receptors mediates the contraction of smooth muscles, increase in capillary permeability due to contraction of terminal venules, and catecholamine release from adrenal medulla, as well as mediating neurotransmission in the central nervous system.
• Pathway: Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);IL-4 Signaling Pathway;GPCRs, Class A Rhodopsin-like;Monoamine GPCRs;Signaling by GPCR;Signal Transduction;Histamine receptors;Amine ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.609
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.197
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hrh1
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype

Zebrafish Information Network

• Gene name: hrh1
• Affected structure: sleep
• Phenotype tag: abnormal
• Phenotype quality: behavioral quality of a process

Gene ontology

• Biological process: inflammatory response;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;phospholipase C-activating G protein-coupled receptor signaling pathway;chemical synaptic transmission;memory;visual learning;positive regulation of inositol trisphosphate biosynthetic process;regulation of vascular permeability;positive regulation of vasoconstriction;inositol phosphate-mediated signaling;regulation of synaptic plasticity;eosinophil chemotaxis;cellular response to histamine;G protein-coupled serotonin receptor signaling pathway
• Cellular component: cytosol;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