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Aliases for HAVCR1 Gene

Aliases for HAVCR1 Gene

  • Hepatitis A Virus Cellular Receptor 1 2 3 5
  • Kidney Injury Molecule 1 2 3 4
  • T-Cell Immunoglobulin Mucin Family Member 1 2 3
  • T-Cell Immunoglobulin Mucin Receptor 1 3 4
  • T-Cell Membrane Protein 1 3 4
  • HAVCR-1 3 4
  • TIMD-1 3 4
  • KIM-1 3 4
  • TIM-1 3 4
  • TIMD1 3 4
  • TIM1 3 4
  • KIM1 3 4
  • TIM 3 4
  • T-Cell Immunoglobulin And Mucin Domain-Containing Protein 1 4
  • T Cell Immunoglobin Domain And Mucin Domain Protein 1 3
  • CD365 3
  • HAVCR 3

External Ids for HAVCR1 Gene

Previous GeneCards Identifiers for HAVCR1 Gene

  • GC05M156391
  • GC05M156437
  • GC05M156389
  • GC05M151544
  • GC05M156456

Summaries for HAVCR1 Gene

Entrez Gene Summary for HAVCR1 Gene

  • 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. Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 4, 12 and 19. [provided by RefSeq, Apr 2015]

GeneCards Summary for HAVCR1 Gene

HAVCR1 (Hepatitis A Virus Cellular Receptor 1) is a Protein Coding gene. Diseases associated with HAVCR1 include Hepatitis and Hepatitis A. Among its related pathways are T Cell Co-Signaling Pathway: Ligand-Receptor Interactions and NF-kappaB Signaling. GO annotations related to this gene include virus receptor activity. An important paralog of this gene is TIMD4.

UniProtKB/Swiss-Prot for HAVCR1 Gene

  • 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.

  • (Microbial infection) Acts as a receptor for hepatitis A virus (PubMed:9658108). Acts as a receptor for ebolavirus and marburg virus by binding exposed phosphatidyl-serine at the surface of virion membrane (PubMed:21536871). Acts as a receptor for Dengue virus by binding exposed phosphatidyl-serine at the surface of virion membrane (PubMed:23084921).

Gene Wiki entry for HAVCR1 Gene

Additional gene information for HAVCR1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HAVCR1 Gene

Genomics for HAVCR1 Gene

Regulatory Elements for HAVCR1 Gene

Enhancers for HAVCR1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05H157048 1.1 FANTOM5 ENCODE 19.5 +19.8 19804 2 ELF3 SOX13 CEBPG RARA TEAD3 NR2F6 SOX5 TEAD1 HLF CEBPB HAVCR1 APOOP1 TIMD4
GH05H157099 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.3 -30.9 -30894 1 ELF3 JUN MAX USF2 CEBPB CHD4 REST EP300 RARA FOSL1 HAVCR2 HAVCR1 NIPAL4 ADAM19 ENSG00000254246 GC05P157083
GH05H157105 1.2 Ensembl ENCODE dbSUPER 8.9 -38.7 -38707 5 HDGF KLF1 TBL1XR1 RB1 POLR2A EED ATF7 RUNX3 IKZF2 CREM HAVCR2 ITK MED7 TIMD4 HAVCR1 ENSG00000254246 PIR42544
GH05H157178 1.3 FANTOM5 Ensembl ENCODE dbSUPER 6.5 -112.2 -112243 6 ZNF664 ZNF112 ITK MED7 HAVCR2 HAVCR1 CYFIP2 FNDC9 FAM71B ENSG00000253980
GH05H157112 1 FANTOM5 Ensembl dbSUPER 8.4 -43.8 -43784 0 HLF HAVCR2 ITK MED7 HAVCR1 ADAM19 NIPAL4 ENSG00000254246 PIR42544
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HAVCR1 on UCSC Golden Path with GeneCards custom track

Genomic Location for HAVCR1 Gene

Chromosome:
5
Start:
156,979,480 bp from pter
End:
157,069,527 bp from pter
Size:
90,048 bases
Orientation:
Minus strand

Genomic View for HAVCR1 Gene

Genes around HAVCR1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HAVCR1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HAVCR1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HAVCR1 Gene

Proteins for HAVCR1 Gene

  • Protein details for HAVCR1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96D42-HAVR1_HUMAN
    Recommended name:
    Hepatitis A virus cellular receptor 1
    Protein Accession:
    Q96D42
    Secondary Accessions:
    • O43656

    Protein attributes for HAVCR1 Gene

    Size:
    359 amino acids
    Molecular mass:
    38720 Da
    Quaternary structure:
    • (Microbial infection) Interacts with hepatitis A virus capsid proteins.
    Miscellaneous:
    • The extracellular part of the protein can be cleaved and detected in urine and is in correlation with the expression in the kidney.

    Three dimensional structures from OCA and Proteopedia for HAVCR1 Gene

neXtProt entry for HAVCR1 Gene

Post-translational modifications for HAVCR1 Gene

  • Glycosylation at posLast=6565, posLast=258258, isoforms=272, and isoforms=286
  • Modification sites at PhosphoSitePlus

Antibody Products

  • R&D Systems Antibodies for HAVCR1 (TIM-1/KIM-1/HAVCR)
  • Cell Signaling Technology (CST) Antibodies for HAVCR1 (TIM-1)

Protein Products

Assay Products

No data available for DME Specific Peptides for HAVCR1 Gene

Domains & Families for HAVCR1 Gene

Gene Families for HAVCR1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Predicted secreted proteins

Protein Domains for HAVCR1 Gene

Graphical View of Domain Structure for InterPro Entry

Q96D42

UniProtKB/Swiss-Prot:

HAVR1_HUMAN :
  • Belongs to the immunoglobulin superfamily. TIM family.
Family:
  • Belongs to the immunoglobulin superfamily. TIM family.
genes like me logo Genes that share domains with HAVCR1: view

Function for HAVCR1 Gene

Molecular function for HAVCR1 Gene

UniProtKB/Swiss-Prot 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.
UniProtKB/Swiss-Prot Function:
(Microbial infection) Acts as a receptor for hepatitis A virus (PubMed:9658108). Acts as a receptor for ebolavirus and marburg virus by binding exposed phosphatidyl-serine at the surface of virion membrane (PubMed:21536871). Acts as a receptor for Dengue virus by binding exposed phosphatidyl-serine at the surface of virion membrane (PubMed:23084921).
UniProtKB/Swiss-Prot Induction:
Up-regulated in the kidney in renal diseases (at protein level).

Phenotypes From GWAS Catalog for HAVCR1 Gene

Gene Ontology (GO) - Molecular Function for HAVCR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001618 virus receptor activity IDA 21536871
genes like me logo Genes that share ontologies with HAVCR1: view
genes like me logo Genes that share phenotypes with HAVCR1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for HAVCR1

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for HAVCR1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
  • R&D Systems cDNA Clones for HAVCR1 (TIM-1/KIM-1/HAVCR)

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HAVCR1 Gene

Localization for HAVCR1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HAVCR1 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HAVCR1 gene
Compartment Confidence
plasma membrane 3
extracellular 3
cytoskeleton 2
lysosome 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HAVCR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0031514 motile cilium IDA 21536871
genes like me logo Genes that share ontologies with HAVCR1: view

Pathways & Interactions for HAVCR1 Gene

genes like me logo Genes that share pathways with HAVCR1: view

Pathways by source for HAVCR1 Gene

1 Cell Signaling Technology pathway for HAVCR1 Gene
1 R&D Systems pathway for HAVCR1 Gene

Gene Ontology (GO) - Biological Process for HAVCR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016032 viral process IEA --
GO:0046718 viral entry into host cell IEA --
genes like me logo Genes that share ontologies with HAVCR1: view

No data available for SIGNOR curated interactions for HAVCR1 Gene

Drugs & Compounds for HAVCR1 Gene

(1) Drugs for HAVCR1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with HAVCR1: view

Transcripts for HAVCR1 Gene

Unigene Clusters for HAVCR1 Gene

Hepatitis A virus cellular receptor 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for HAVCR1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
  • R&D Systems cDNA Clones for HAVCR1 (TIM-1/KIM-1/HAVCR)

Alternative Splicing Database (ASD) splice patterns (SP) for HAVCR1 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10
SP1:
SP2: - -
SP3: - -
SP4: -

Relevant External Links for HAVCR1 Gene

GeneLoc Exon Structure for
HAVCR1
ECgene alternative splicing isoforms for
HAVCR1

Expression for HAVCR1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HAVCR1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HAVCR1 Gene

This gene is overexpressed in Kidney - Cortex (x21.3).

Protein differential expression in normal tissues from HIPED for HAVCR1 Gene

This gene is overexpressed in Milk (51.6) and Pancreatic juice (17.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HAVCR1 Gene



Protein tissue co-expression partners for HAVCR1 Gene

NURSA nuclear receptor signaling pathways regulating expression of HAVCR1 Gene:

HAVCR1

SOURCE GeneReport for Unigene cluster for HAVCR1 Gene:

Hs.129711

mRNA Expression by UniProt/SwissProt for HAVCR1 Gene:

Q96D42-HAVR1_HUMAN
Tissue specificity: Widely expressed, with highest levels in kidney and testis. Expressed by activated CD4+ T-cells during the development of helper T-cells responses.

Evidence on tissue expression from TISSUES for HAVCR1 Gene

  • Kidney(4.7)
  • Liver(4.3)
  • Urine(3)
  • Blood(2.4)
genes like me logo Genes that share expression patterns with HAVCR1: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for HAVCR1 Gene

Orthologs for HAVCR1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HAVCR1 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia HAVCR1 33 34
  • 72.93 (n)
chimpanzee
(Pan troglodytes)
Mammalia HAVCR1 34
  • 67 (a)
OneToOne
cow
(Bos Taurus)
Mammalia MGC137099 34
  • 48 (a)
OneToMany
-- 34
  • 40 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Havcr1 34
  • 38 (a)
OneToMany
BC053393 34
  • 33 (a)
OneToMany
Timd2 34
  • 31 (a)
OneToMany
Gm12169 34
  • 30 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia HAVCR1 34
  • 26 (a)
OneToOne
chicken
(Gallus gallus)
Aves HAVCR1 33 34
  • 54.72 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 2 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii timd4 34
  • 19 (a)
OneToMany
Species where no ortholog for HAVCR1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HAVCR1 Gene

ENSEMBL:
Gene Tree for HAVCR1 (if available)
TreeFam:
Gene Tree for HAVCR1 (if available)

Paralogs for HAVCR1 Gene

Paralogs for HAVCR1 Gene

(1) SIMAP similar genes for HAVCR1 Gene using alignment to 7 proteins:

Pseudogenes.org Pseudogenes for HAVCR1 Gene

genes like me logo Genes that share paralogs with HAVCR1: view

Variants for HAVCR1 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for HAVCR1 Gene

HAVR1_HUMAN-Q96D42
Infection by hepatitis A virus (HAV) protects individuals from atopy if they carry insertion of the variants Met-Thr-Thr-Val-Pro-157 and Met-Thr-Thr-Thr-Val-Pro-157. Modernisation has led to a reduction in HAV seroprevalence and thus, may be, to an increase of expression of atopy, such as asthma, allergic rhinitis and atopic dermatitis. Allelic variation does not affect HAV-infection rates in Caucasians, Asians and African Americans.

Sequence variations from dbSNP and Humsavar for HAVCR1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs1000029837 -- 156,990,511(+) GACTG(A/G)ATCAA intron-variant
rs1000034514 -- 157,036,434(+) CGATC(A/G)TGCCA intron-variant
rs1000052924 -- 157,049,120(+) GCTGG(C/T)TGAGG nc-transcript-variant, reference, synonymous-codon
rs1000104900 -- 157,048,784(+) GAGAT(A/C/T)GTGCC intron-variant
rs1000106982 -- 157,051,970(+) TCTTC(A/G)GAGCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HAVCR1 Gene

Variant ID Type Subtype PubMed ID
esv2730954 CNV deletion 23290073
esv3575892 CNV gain 25503493
esv3607302 CNV gain 21293372
esv3607306 CNV gain 21293372
nsv1016820 CNV gain 25217958
nsv474311 CNV novel sequence insertion 20440878
nsv477873 CNV novel sequence insertion 20440878

Variation tolerance for HAVCR1 Gene

Residual Variation Intolerance Score: 95% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.71; 89.30% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HAVCR1 Gene

Human Gene Mutation Database (HGMD)
HAVCR1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HAVCR1

Disorders for HAVCR1 Gene

MalaCards: The human disease database

(18) MalaCards diseases for HAVCR1 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hepatitis
  • acute and subacute liver necrosis
hepatitis a
  • viral hepatitis a
atopy
  • atopic hypersensitivity
dermis tumor
  • neoplasm of dermis
asthma
  • asthma, protection against
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for HAVCR1

Genetic Association Database (GAD)
HAVCR1
Human Genome Epidemiology (HuGE) Navigator
HAVCR1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HAVCR1
genes like me logo Genes that share disorders with HAVCR1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HAVCR1 Gene

Publications for HAVCR1 Gene

  1. The human homolog of HAVcr-1 codes for a hepatitis A virus cellular receptor. (PMID: 9658108) Feigelstock D … Kaplan GG (Journal of virology 1998) 2 3 4 22 60
  2. Association between TIM-1 gene polymorphisms and allergic rhinitis in a Han Chinese population. (PMID: 20232767) Mou Z … Li H (Journal of investigational allergology & clinical immunology 2010) 3 22 45 60
  3. Fine mapping of T-cell immunoglobulin mucin domain gene 1 failed to detect a significant association with multiple sclerosis. (PMID: 20070602) Grabmer C … Gassner C (Tissue antigens 2010) 3 22 45 60
  4. Family-based association study of Tim-1 and Tim-3 gene polymorphisms with childhood asthma in Chinese trios. (PMID: 19494522) Wu QW … Hu LH (International archives of allergy and immunology 2009) 3 22 45 60
  5. Association analysis of TIM-1 -232G > A and 5383_5397 insertion/deletion polymorphisms with childhood asthma and total serum immunoglobulin E levels in middle China. (PMID: 19476019) Wu Q … Kong L (Journal of investigational allergology & clinical immunology 2009) 3 22 45 60

Products for HAVCR1 Gene

Sources for HAVCR1 Gene

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