HAVCR1
protein-codinghepatitis A virus cellular receptor 1, the group of V-set domain containing|CD molecules
Gene summary
The protein encoded by this gene is a membrane receptor for both human hepatitis A virus (HHAV) and TIMD4. The encoded protein may be involved in the moderation of asthma and allergic diseases. The reference genome represents an allele that retains a MTTVP amino acid segment that confers protection against atopy in HHAV seropositive individuals. The protein is a receptor for multiple other viruses, including Ebola virus, Marburg virus, Dengue virus, and Zika virus and is a possible entry factor for SARS-CoV-2 and other coronaviruses. [provided by RefSeq, Sep 2021]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~42.7 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 HAVCR1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001173393.3. 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 | 4 | 2 | 7 | ||
| missense | 46 | 8 | 4 | 58 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 48 | 12 | 6 | 66 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001166864.1 | 8 | MANE Select | |
| Ensembl | ENSP00000427898.1 | 8 | MANE Select | |
| RefSeq | NP_001295085.1 | 7 | Standard | |
| RefSeq | NP_036338.2 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ebola Virus Pathway on Host
- Ebola Virus Pathway on Host
Biological Process
- viral entry into host cell
Molecular Function
- virus receptor activity
Cellular Component
- integral component of membrane
- motile cilium
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000339252
- Coding exons
- 8
- Length
- 29707
- Individuals with no LoFs
- 124657
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 137
- Defined
- 124794
- p
- 0.000549
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.00775 | 204 | 204 | 1.00 | 0.0000117 | 2315 |
| Missense (PolyPhen) | 24 | 25.915 | 0.9261 | 308 | ||
| Synonymous | -1.32 | 94 | 79.1 | 1.19 | 0.00000498 | 779 |
| Loss of Function | 0.833 | 11 | 14.4 | 0.763 | 7.61e-7 | 167 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00046 | 0.00045 | rare |
| Latino/Admixed American | 0.00035 | 0.00029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00064 | 0.00064 | rare |
| South Asian | 0.0015 | 0.0014 | notable |
| Other | 0.00066 | 0.00066 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in T-helper cell development and the regulation of asthma and allergic diseases. Receptor for TIMD4 (By similarity). May play a role in kidney injury and repair. {ECO:0000250, ECO:0000269|PubMed:17471468}.; FUNCTION: (Microbial infection) Acts as a receptor for Ebolavirus and Marburg virus by binding exposed phosphatidyl-serine at the surface of virion membrane. {ECO:0000269|PubMed:21536871}.;
Intolerance Scores
- LoFtool
- 0.951
- RVIS EVS
- 0.8
- RVIS percentile EVS
- 87.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0172
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |