HRH1

Chr 3

histamine receptor H1

Also known as: H1-R, H1R, HH1R, hisH1

NCBI Gene: 3269ENSG00000196639UniProt: P35367OMIM: 600167

The histamine H1 receptor is a G-protein-coupled receptor that mediates smooth muscle contraction, increases capillary permeability, and regulates neurotransmission in the central nervous system including circadian rhythms and cognitive functions. Mutations cause autosomal recessive nonsyndromic intellectual disability with developmental delays typically apparent in early childhood. This gene shows low constraint to loss-of-function variants based on population data.

OMIMResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 1.16
Clinical Summary— HRH1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
35 unique Pathogenic / Likely Pathogenic· 32 VUS of 77 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.16LOEUF
pLI 0.000
Z-score 1.11
OE 0.70 (0.44–1.16)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.81Z-score
OE missense 0.86 (0.78–0.96)
238 obs / 276.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.70 (0.44–1.16)
0≤0.351.4
Missense OE0.86 (0.78–0.96)
0≤0.61.4
Synonymous OE1.07
0≤1.21.6
LoF obs/exp: 11 / 15.8Missense obs/exp: 238 / 276.0Syn Z: -0.61
DN
0.80top 25%
GOF
0.77top 25%
LOF
0.2483th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

77 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic33
Likely Pathogenic2
VUS32
Likely Benign4
Benign4
33
Pathogenic
2
Likely Pathogenic
32
VUS
4
Likely Benign
4
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
33
0
33
Likely Pathogenic
0
0
2
0
2
VUS
0
30
2
0
32
Likely Benign
0
2
1
1
4
Benign
0
4
0
0
4
Total03638175

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

HRH1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients