Aliases for HAPLN1 Gene

Aliases for HAPLN1 Gene

  • Hyaluronan And Proteoglycan Link Protein 1 2 3 4 5
  • Cartilage-Linking Protein 1 3 4
  • Proteoglycan Link Protein 3 4
  • Cartilage Link Protein 2 3
  • Cartilage-Link Protein 3 4
  • CRTL1 3 4
  • Cartilage Linking Protein 1 2
  • HAPLN1 5
  • CRT1 3

External Ids for HAPLN1 Gene

Previous HGNC Symbols for HAPLN1 Gene

  • CRTL1

Previous GeneCards Identifiers for HAPLN1 Gene

  • GC05M083020
  • GC05M082972
  • GC05M078141
  • GC05M082933

Summaries for HAPLN1 Gene

GeneCards Summary for HAPLN1 Gene

HAPLN1 (Hyaluronan And Proteoglycan Link Protein 1) is a Protein Coding gene. Diseases associated with HAPLN1 include Juvenile Rheumatoid Arthritis and Cerebral Creatine Deficiency Syndrome. Among its related pathways are Integrin Pathway and Degradation of the extracellular matrix. Gene Ontology (GO) annotations related to this gene include extracellular matrix structural constituent and hyaluronic acid binding. An important paralog of this gene is HAPLN3.

UniProtKB/Swiss-Prot Summary for HAPLN1 Gene

  • Stabilizes the aggregates of proteoglycan monomers with hyaluronic acid in the extracellular cartilage matrix.

Gene Wiki entry for HAPLN1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HAPLN1 Gene

Genomics for HAPLN1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HAPLN1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J083721 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 261.5 +0.6 564 4.9 EZH2 ZNF654 ZNF600 ZNF580 POLR2A ZIC2 ZBTB10 REST TRIM22 ZNF341 HAPLN1 lnc-EDIL3-5 LOC105379055 VCAN
GH05J083918 Enhancer 0.7 FANTOM5 Ensembl ENCODE 27.6 -198.0 -197991 2 JUND EP300 HAPLN1 LOC107986386 MN309174-540 EDIL3
GH05J083923 Enhancer 0.8 FANTOM5 Ensembl ENCODE 17.9 -204.0 -203970 3.7 JUND CTCF BHLHE40 POLR2A EP300 CEBPB HAPLN1 RNU6-448P LOC107986386 MN309174-540 EDIL3
GH05J084259 Enhancer 0.5 Ensembl 10.9 -538.8 -538791 0.8 SPI1 NR2F1 IKZF1 IKZF2 MTA2 RUNX3 RELB SCRT2 HAPLN1 piR-31508-045 piR-55809-031 EDIL3
GH05J083913 Enhancer 0.3 Ensembl 17.6 -193.5 -193492 1.4 CEBPB HAPLN1 LOC107986386 MN309174-540 EDIL3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HAPLN1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HAPLN1

Top Transcription factor binding sites by QIAGEN in the HAPLN1 gene promoter:
  • Chx10
  • CUTL1
  • Lhx3a
  • LHX3b
  • NRSF form 1
  • NRSF form 2
  • POU2F1
  • POU2F1a
  • POU6F1 (c2)
  • RORalpha1

Genomic Locations for HAPLN1 Gene

Latest Assembly
83,406 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
83,051 bases
Minus strand

(GRCh37/hg19 by Ensembl)
83,809 bases
Minus strand

Genomic View for HAPLN1 Gene

Genes around HAPLN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HAPLN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HAPLN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HAPLN1 Gene

Proteins for HAPLN1 Gene

  • Protein details for HAPLN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Hyaluronan and proteoglycan link protein 1
    Protein Accession:
    Secondary Accessions:
    • B2R9A9

    Protein attributes for HAPLN1 Gene

    354 amino acids
    Molecular mass:
    40166 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HAPLN1 Gene

Post-translational modifications for HAPLN1 Gene

  • Glycosylation at Asn21 and Asn56
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • HPLN1_HUMAN (1380)

No data available for DME Specific Peptides for HAPLN1 Gene

Domains & Families for HAPLN1 Gene

Gene Families for HAPLN1 Gene

Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for HAPLN1 Gene

  • Immunoglobulin V-set
  • Immunoglobulin V-type
  • Link domain

Suggested Antigen Peptide Sequences for HAPLN1 Gene

GenScript: Design optimal peptide antigens:
  • Proteoglycan link protein (HPLN1_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the HAPLN family.
  • Belongs to the HAPLN family.
genes like me logo Genes that share domains with HAPLN1: view

Function for HAPLN1 Gene

Molecular function for HAPLN1 Gene

UniProtKB/Swiss-Prot Function:
Stabilizes the aggregates of proteoglycan monomers with hyaluronic acid in the extracellular cartilage matrix.

Phenotypes From GWAS Catalog for HAPLN1 Gene

Gene Ontology (GO) - Molecular Function for HAPLN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005540 hyaluronic acid binding IEA --
GO:0030021 extracellular matrix structural constituent conferring compression resistance RCA 20551380
genes like me logo Genes that share ontologies with HAPLN1: view
genes like me logo Genes that share phenotypes with HAPLN1: view

Animal Models for HAPLN1 Gene

MGI Knock Outs for HAPLN1:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HAPLN1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HAPLN1 Gene

Localization for HAPLN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HAPLN1 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

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 HAPLN1 gene
Compartment Confidence
extracellular 5
plasma membrane 2
cytoskeleton 2
nucleus 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HAPLN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA,TAS --
GO:0031012 extracellular matrix TAS,IBA 21873635
GO:0045202 synapse IEA --
GO:0062023 colocalizes_with collagen-containing extracellular matrix HDA 20551380
genes like me logo Genes that share ontologies with HAPLN1: view

Pathways & Interactions for HAPLN1 Gene

PathCards logo

SuperPathways for HAPLN1 Gene

SuperPathway Contained pathways
1 Integrin Pathway
2 ERK Signaling
3 Phospholipase-C Pathway
4 Articular Cartilage Extracellular Matrix Pathway
5 ECM proteoglycans
genes like me logo Genes that share pathways with HAPLN1: view

Pathways by source for HAPLN1 Gene

2 Reactome pathways for HAPLN1 Gene
1 GeneGo (Thomson Reuters) pathway for HAPLN1 Gene
  • Cell adhesion_Cell-matrix glycoconjugates
1 R&D Systems pathway for HAPLN1 Gene
13 Qiagen pathways for HAPLN1 Gene
  • ERK Signaling
  • FAK1 Signaling
  • GnRH Signaling
  • ILK Signaling
  • Inhibition of Angiogenesis by TSP1

SIGNOR curated interactions for HAPLN1 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for HAPLN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IBA 21873635
GO:0007155 cell adhesion IEA --
GO:0007417 central nervous system development IBA 21873635
GO:0030198 extracellular matrix organization TAS --
genes like me logo Genes that share ontologies with HAPLN1: view

Drugs & Compounds for HAPLN1 Gene

(3) Drugs for HAPLN1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Hyaluronic acid Approved, Vet_approved Pharma Target, binder 827

(4) Additional Compounds for HAPLN1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HAPLN1: view

Transcripts for HAPLN1 Gene

mRNA/cDNA for HAPLN1 Gene

7 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HAPLN1

Alternative Splicing Database (ASD) splice patterns (SP) for HAPLN1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b · 6c ^ 7a · 7b · 7c ^ 8a · 8b
SP1: - - - -
SP2: -
SP4: - - -
SP5: - -

Relevant External Links for HAPLN1 Gene

GeneLoc Exon Structure for

Expression for HAPLN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HAPLN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HAPLN1 Gene

This gene is overexpressed in Artery - Aorta (x10.0) and Artery - Coronary (x9.2).

Protein differential expression in normal tissues from HIPED for HAPLN1 Gene

This gene is overexpressed in Amniocyte (13.8), Frontal cortex (10.9), Synovial fluid (10.5), Brain (8.1), Bone marrow mesenchymal stem cell (7.1), and Vitreous humor (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HAPLN1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HAPLN1

SOURCE GeneReport for Unigene cluster for HAPLN1 Gene:


mRNA Expression by UniProt/SwissProt for HAPLN1 Gene:

Tissue specificity: Widely expressed. Weakly expressed in the brain.

Evidence on tissue expression from TISSUES for HAPLN1 Gene

  • Bone(2.9)
  • Nervous system(2.8)
  • Heart(2.2)
genes like me logo Genes that share expression patterns with HAPLN1: view

Primer products for research

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for HAPLN1 Gene

Orthologs for HAPLN1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HAPLN1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HAPLN1 29 30
  • 99.62 (n)
(Canis familiaris)
Mammalia HAPLN1 29 30
  • 93.03 (n)
(Bos Taurus)
Mammalia HAPLN1 29 30
  • 92.75 (n)
(Monodelphis domestica)
Mammalia HAPLN1 30
  • 92 (a)
(Ornithorhynchus anatinus)
Mammalia HAPLN1 30
  • 91 (a)
(Mus musculus)
Mammalia Hapln1 29 16 30
  • 89.08 (n)
(Rattus norvegicus)
Mammalia Hapln1 29
  • 88.7 (n)
(Gallus gallus)
Aves HAPLN1 29 30
  • 81.07 (n)
(Anolis carolinensis)
Reptilia HAPLN1 30
  • 80 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia hapln1 29
  • 76.38 (n)
(Danio rerio)
Actinopterygii hapln1b 29 30
  • 70.08 (n)
Species where no ortholog for HAPLN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for HAPLN1 Gene

Gene Tree for HAPLN1 (if available)
Gene Tree for HAPLN1 (if available)
Evolutionary constrained regions (ECRs) for HAPLN1: view image
Alliance of Genome Resources:
Additional Orthologs for HAPLN1

Paralogs for HAPLN1 Gene

Paralogs for HAPLN1 Gene

(8) SIMAP similar genes for HAPLN1 Gene using alignment to 7 proteins:

  • D6RC59_HUMAN
  • D6RG04_HUMAN
genes like me logo Genes that share paralogs with HAPLN1: view

Variants for HAPLN1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HAPLN1 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
VAR_036168 A colorectal cancer sample p.Arg333His
rs6864342 -- p.Asn281Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for HAPLN1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for HAPLN1 Gene

Variant ID Type Subtype PubMed ID
esv2660307 CNV deletion 23128226
esv2730402 CNV deletion 23290073
esv3605639 CNV loss 21293372
nsv1015852 CNV gain 25217958
nsv327409 CNV deletion 16902084
nsv4904 CNV insertion 18451855
nsv830367 CNV gain+loss 17160897

Variation tolerance for HAPLN1 Gene

Residual Variation Intolerance Score: 68.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.02; 21.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HAPLN1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HAPLN1 Gene

Disorders for HAPLN1 Gene

MalaCards: The human disease database

(12) MalaCards diseases for HAPLN1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
juvenile rheumatoid arthritis
  • acute juvenile rheumatoid arthritis
cerebral creatine deficiency syndrome
  • deficiency, cerebral creatine, syndrome
  • psach
cerebral creatine deficiency syndrome 3
  • ccds3
  • degenerative arthritis
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HAPLN1

Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with HAPLN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HAPLN1 Gene

Publications for HAPLN1 Gene

  1. Complete amino acid sequence of human cartilage link protein (CRTL1) deduced from cDNA clones and chromosomal assignment of the gene. (PMID: 2286376) Osborne-Lawrence SL … Duby AD (Genomics 1990) 2 3 4 22
  2. A hyaluronan binding link protein gene family whose members are physically linked adjacent to chondroitin sulfate proteoglycan core protein genes: the missing links. (PMID: 12663660) Spicer AP … Bowling RA (The Journal of biological chemistry 2003) 3 4 22
  3. The brain link protein-1 (BRAL1): cDNA cloning, genomic structure, and characterization as a novel link protein expressed in adult brain. (PMID: 11027579) Hirakawa S … Ninomiya Y (Biochemical and biophysical research communications 2000) 3 4 22
  4. The primary structure of human cartilage link protein. (PMID: 2320422) Dudhia J … Hardingham TE (Nucleic acids research 1990) 2 3 4
  5. A Large-scale genetic association study of esophageal adenocarcinoma risk. (PMID: 20453000) Liu CY … Christiani DC (Carcinogenesis 2010) 3 40

Products for HAPLN1 Gene

Sources for HAPLN1 Gene