HAPLN1

gene
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Summary

HAPLN1 (hyaluronan and proteoglycan link protein 1, HGNC:2380) is a protein-coding gene on chromosome 5q14.3, encoding Hyaluronan and proteoglycan link protein 1 (P10915). Stabilizes the aggregates of proteoglycan monomers with hyaluronic acid in the extracellular cartilage matrix.

Predicted to enable hyaluronic acid binding activity. Predicted to be an extracellular matrix structural constituent conferring compression resistance. Predicted to be involved in central nervous system development and skeletal system development. Located in collagen-containing extracellular matrix.

Source: NCBI Gene 1404 — RefSeq curated summary.

At a glance

  • GWAS associations: 14
  • Clinical variants (ClinVar): 55 total
  • MANE Select transcript: NM_001884

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2380
Approved symbolHAPLN1
Namehyaluronan and proteoglycan link protein 1
Location5q14.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000145681
Ensembl biotypeprotein_coding
OMIM115435
Entrez1404

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 10 protein_coding

ENST00000274341, ENST00000503117, ENST00000504713, ENST00000508307, ENST00000510978, ENST00000514416, ENST00000515590, ENST00000875523, ENST00000936313, ENST00000936314

RefSeq mRNA: 1 — MANE Select: NM_001884 NM_001884

CCDS: CCDS4061

Canonical transcript exons

ENST00000274341 — 5 exons

ExonStartEnd
ENSE000009715938365245383652824
ENSE000010051188367342483673549
ENSE000011205408363780583641785
ENSE000011636118372078983720855
ENSE000037897708364436383644665

Expression profiles

Bgee: expression breadth ubiquitous, 172 present calls, max score 99.95.

FANTOM5 (CAGE): breadth broad, TPM avg 16.6134 / max 824.1748, expressed in 600 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
6236510.4147525
623683.6895394
623691.1077253
623660.7471166
623670.5379191
623620.062521
623640.044421
623630.00955

Top tissues by expression

271 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
tibiaUBERON:000097999.95gold quality
cartilage tissueUBERON:000241899.74gold quality
placentaUBERON:000198789.61gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.39gold quality
endothelial cellCL:000011588.28gold quality
colonic epitheliumUBERON:000039787.74gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.35gold quality
buccal mucosa cellCL:000233684.46gold quality
mucosa of sigmoid colonUBERON:000499382.78gold quality
jejunal mucosaUBERON:000039981.55gold quality
rectumUBERON:000105280.94gold quality
tracheaUBERON:000312680.51gold quality
right coronary arteryUBERON:000162578.58gold quality
colonic mucosaUBERON:000031778.29gold quality
calcaneal tendonUBERON:000370176.53gold quality
ascending aortaUBERON:000149675.86gold quality
thoracic aortaUBERON:000151575.40gold quality
embryoUBERON:000092273.32gold quality
mucosa of transverse colonUBERON:000499172.98gold quality
duodenumUBERON:000211472.82gold quality
mucosa of paranasal sinusUBERON:000503072.49gold quality
prefrontal cortexUBERON:000045171.87gold quality
left coronary arteryUBERON:000162671.70gold quality
periodontal ligamentUBERON:000826671.51silver quality
coronary arteryUBERON:000162171.40gold quality
jejunumUBERON:000211571.14gold quality
tendonUBERON:000004370.92gold quality
trabecular bone tissueUBERON:000248370.54gold quality
descending thoracic aortaUBERON:000234570.03gold quality
ventricular zoneUBERON:000305369.29gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 11.

ExperimentMarker?Max mean expression
E-HCAD-23yes2113.70
E-MTAB-6701yes1824.95
E-HCAD-24yes1764.27
E-MTAB-9388yes1677.57
E-MTAB-7008yes921.35
E-MTAB-10018yes654.89
E-HCAD-11yes605.12
E-MTAB-3929yes289.58
E-CURD-46yes21.67
E-CURD-112yes7.95
E-ANND-3yes5.34
E-MTAB-8271no2223.59

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): RUNX1, RUNX2, SOX9

miRNA regulators (miRDB)

259 targeting HAPLN1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-340-5P100.0072.504437
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4425100.0067.591049
HSA-MIR-656-3P100.0072.152788
HSA-MIR-5692A100.0074.406850
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-9-5P100.0072.282361
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-511-3P99.9968.851467
HSA-MIR-366299.9973.825684
HSA-MIR-223-3P99.9970.141140
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-477599.9875.006394
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882

Literature-anchored findings (GeneRIF, showing 18)

  • link protein may function as a stabilizer of the interaction between aggrecan and hyaluronan in cartilage and between versican and hyaluronan in many tissues (PMID:14724283)
  • SOX9 is a key regulator of CRTL1 (PMID:15456769)
  • cLP and versican did not bind directly to each other in solution yet formed ternary complexes with hyaluronan (PMID:15590670)
  • Overexpression of HAPLN1 and its SP-IgV domain increases tumorigenic properties of mesothelioma. Thus, targeting the SP-IgV domain may be one of the therapeutic approaches in cancer treatment. (PMID:19351750)
  • An in vitro model of perineuronal nets has been developed demonstrating that cartilage link protein (along with hyaluronan synthase) are necessary for their formation. (PMID:20584105)
  • Single-nucleotide polymorphism in the hyaluronan and proteoglycan link protein 1 (HAPLN1) gene is associated with spinal osteophyte formation and disc degeneration in Japanese women. (PMID:20953637)
  • HAPLN1 is overexpressed in metastatic melanoma and is secreted exclusively by the tumor cells (PMID:22159717)
  • CSGalNAcT-1 and Hapln-1 may play important roles in the pathogenesis of Kashin-Beck disease and osteoarthritis. (PMID:23748413)
  • HAPLN1 reflects a signaling network leading to stemness, mesenchymal commitment and hepatocellular carcinoma progression (PMID:27191501)
  • HAPLN1 is produced in bone marrow stromal cells from multiple myeloma patients and can activate bortezomib-resistant NF-kappaB. (PMID:29279332)
  • A novel role of HAPLN1 loss was reported in the aging lymphatic ECM in mediating lymphatic endothelial permeability, thus permitting melanoma cells to escape from the lymphatic system to distant metastatic sites. (PMID:30279172)
  • A Role for HAPLN1 During Phenotypic Modulation of Human Lung Fibroblasts In Vitro. (PMID:33064036)
  • A Hyaluronan and Proteoglycan Link Protein 1 Matrikine: Role of Matrix Metalloproteinase 2 in Multiple Myeloma NF-kappaB Activation and Drug Resistance. (PMID:35604822)
  • HAPLN1 Affects Cell Viability and Promotes the Pro-Inflammatory Phenotype of Fibroblast-Like Synoviocytes. (PMID:35720292)
  • Hyaluronan and Proteoglycan Link Protein 1 Activates the BMP4/Smad1/5/8 Signaling Pathway to Promote Osteogenic Differentiation: an Implication in Fracture Healing. (PMID:36737556)
  • HAPLN1 matrikine: a bone marrow homing factor linked to poor outcomes in patients with MM. (PMID:37647592)
  • Probing binding and occlusion of substrate in the human creatine transporter-1 by computation and mutagenesis. (PMID:38032325)
  • Analysis of ANO6, HAPLN1, and EDIL3 Polymorphisms in Patients with Ankylosing Spondylitis in a Chinese Han Population: A Case-Control Study. (PMID:39358671)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriohapln1bENSDARG00000068516
ENSDARG00000102395
mus_musculusHapln1ENSMUSG00000021613
rattus_norvegicusHapln1ENSRNOG00000032002

Paralogs (7): VCAN (ENSG00000038427), NCAN (ENSG00000130287), BCAN (ENSG00000132692), HAPLN2 (ENSG00000132702), HAPLN3 (ENSG00000140511), ACAN (ENSG00000157766), HAPLN4 (ENSG00000187664)

Protein

Protein identifiers

Hyaluronan and proteoglycan link protein 1P10915 (reviewed: P10915)

Alternative names: Cartilage-linking protein 1, Proteoglycan link protein

All UniProt accessions (7): D6RAK7, D6RBS1, D6RBX9, D6RC59, D6RFI7, D6RG04, P10915

UniProt curated annotations — full annotation on UniProt →

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

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

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

Similarity. Belongs to the HAPLN family.

RefSeq proteins (1): NP_001875* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000538Link_domDomain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR013106Ig_V-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR016186C-type_lectin-like/link_sfHomologous_superfamily
IPR016187CTDL_foldHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR050691Hyaluronan_bind_ProteoglycanFamily

Pfam: PF00193, PF07686

UniProt features (15 total): disulfide bond 5, domain 3, sequence variant 2, glycosylation site 2, propeptide 1, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P10915-F189.640.81

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (5): 279–349, 304–325, 61–139, 181–252, 205–226

Glycosylation sites (2): 21, 56

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-3000178ECM proteoglycans

MSigDB gene sets: 254 (showing top): HNF3ALPHA_Q6, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, TATTATA_MIR374, MEF2_02, GGGTGGRR_PAX4_03, NAISHIRO_CTNNB1_TARGETS_WITH_LEF1_MOTIF, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, TCF4_Q5, MODULE_205, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT, WTGAAAT_UNKNOWN, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, TGACATY_UNKNOWN, IRF_Q6, GOMF_GLYCOSAMINOGLYCAN_BINDING

GO Biological Process (3): skeletal system development (GO:0001501), cell adhesion (GO:0007155), central nervous system development (GO:0007417)

GO Molecular Function (2): hyaluronic acid binding (GO:0005540), extracellular matrix structural constituent conferring compression resistance (GO:0030021)

GO Cellular Component (5): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), extracellular matrix (GO:0031012), synapse (GO:0045202), perineuronal net (GO:0072534)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Extracellular matrix organization1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
system development2
cellular process1
nervous system development1
carboxylic acid binding1
extracellular matrix structural constituent1
cellular anatomical structure1
external encapsulating structure1
cell junction1
perisynaptic extracellular matrix1

Protein interactions and networks

STRING

1462 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HAPLN1ACANP16112925
HAPLN1COL9A1P20849818
HAPLN1COL11A1P12107774
HAPLN1COL9A2Q14055765
HAPLN1SLC6A8P48029726
HAPLN1COL2A1P02458717
HAPLN1COMPP49747703
HAPLN1COL11A2P13942680
HAPLN1EDIL3O43854644
HAPLN1HAS3O00219611
HAPLN1MATN3O15232590
HAPLN1LUMP51884581
HAPLN1PRELPP51888580
HAPLN1GATMP50440573
HAPLN1IHHQ14623564

IntAct

14 interactions, top by confidence:

ABTypeScore
ADGRA2HAPLN1psi-mi:“MI:0915”(physical association)0.400
HAPLN1CNTN4psi-mi:“MI:0915”(physical association)0.400
HAPLN1MPIG6Bpsi-mi:“MI:0915”(physical association)0.400
IGDCC4HAPLN1psi-mi:“MI:0915”(physical association)0.400
IL1RL1HAPLN1psi-mi:“MI:0915”(physical association)0.400
MICAHAPLN1psi-mi:“MI:0915”(physical association)0.400
HAPLN1PRTGpsi-mi:“MI:0915”(physical association)0.400
AGERHAPLN1psi-mi:“MI:0915”(physical association)0.400
HAPLN1TNFRSF11Bpsi-mi:“MI:0915”(physical association)0.400
TREML2HAPLN1psi-mi:“MI:0915”(physical association)0.400
MAPTNCANpsi-mi:“MI:0914”(association)0.350
PRNPWDR91psi-mi:“MI:0914”(association)0.350
AFG2BMMP24OSpsi-mi:“MI:0914”(association)0.350

BioGRID (5): HAPLN1 (Reconstituted Complex), HAPLN1 (Affinity Capture-MS), HAPLN1 (Affinity Capture-MS), HAPLN1 (Affinity Capture-MS), APP (Reconstituted Complex)

ESM2 similar proteins: A1A4K5, A2ARA8, A7XY94, A8MWY0, O08859, O15041, O42237, O54890, O70309, P03994, P05106, P07354, P10859, P10915, P15396, P18084, P21860, P22413, P26009, P35436, P53708, P55252, P70207, P70275, P80747, P98066, Q00959, Q00960, Q01097, Q07441, Q13224, Q13822, Q28381, Q3UZV7, Q5R1P3, Q5RB22, Q61526, Q64610, Q6BEA0, Q6P9A2

Diamond homologs: A0A182C2Z2, C6KFA3, F1RWC3, O08628, O08859, O14594, O14786, O35276, O35375, O43897, O57382, O57460, O60462, O60494, O70244, P03994, P07354, P07897, P07898, P10859, P10915, P13497, P13608, P13611, P14745, P16112, P25723, P28824, P42674, P55066, P55067, P55252, P79795, P97333, P98063, P98065, P98066, P98068, P98069, P98070

SIGNOR signaling

7 interactions.

AEffectBMechanism
MMP2“down-regulates quantity by destabilization”HAPLN1cleavage
MMP9“down-regulates quantity by destabilization”HAPLN1cleavage
MMP7“down-regulates quantity by destabilization”HAPLN1cleavage
MMP3“down-regulates quantity by destabilization”HAPLN1cleavage
MMP10“down-regulates quantity by destabilization”HAPLN1cleavage

Disease & clinical

Clinical variants and AI predictions

ClinVar

55 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance49
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1257 predictions. Top by Δscore:

VariantEffectΔscore
5:83641782:CGGC:Cacceptor_gain1.0000
5:83641784:GCC:Gacceptor_loss1.0000
5:83641786:C:CCacceptor_gain1.0000
5:83641786:CT:Cacceptor_loss1.0000
5:83641787:T:Aacceptor_loss1.0000
5:83644426:AGTT:Adonor_gain1.0000
5:83644429:T:TAdonor_gain1.0000
5:83644556:CAG:Cdonor_gain1.0000
5:83644663:CAC:Cacceptor_gain1.0000
5:83644671:C:Tacceptor_gain1.0000
5:83652449:ATACC:Adonor_loss1.0000
5:83652450:TA:Tdonor_loss1.0000
5:83652451:A:ACdonor_gain1.0000
5:83652451:A:Tdonor_loss1.0000
5:83652452:C:CCdonor_gain1.0000
5:83652653:T:TAdonor_gain1.0000
5:83652654:C:Adonor_gain1.0000
5:83652820:TTCTG:Tacceptor_gain1.0000
5:83652822:CTG:Cacceptor_gain1.0000
5:83652825:C:CCacceptor_gain1.0000
5:83652831:T:Cacceptor_gain1.0000
5:83652831:T:TCacceptor_gain1.0000
5:83673418:CCTTA:Cdonor_loss1.0000
5:83673419:CTTA:Cdonor_loss1.0000
5:83673420:TTA:Tdonor_loss1.0000
5:83673421:TAC:Tdonor_loss1.0000
5:83673422:A:Tdonor_loss1.0000
5:83673423:C:CTdonor_loss1.0000
5:83673548:CA:Cacceptor_gain1.0000
5:83673562:C:CTacceptor_gain1.0000

AlphaMissense

2312 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:83652684:A:GW81R1.000
5:83652684:A:TW81R1.000
5:83641514:G:CC349W0.999
5:83641515:C:TC349Y0.999
5:83641637:C:AW308C0.999
5:83641637:C:GW308C0.999
5:83641639:A:GW308R0.999
5:83641639:A:TW308R0.999
5:83641724:A:CC279W0.999
5:83641725:C:TC279Y0.999
5:83644382:A:CC252W0.999
5:83644595:A:CC181W0.999
5:83652509:C:GC139S0.999
5:83652510:A:GC139R0.999
5:83652510:A:TC139S0.999
5:83652682:C:AW81C0.999
5:83652682:C:GW81C0.999
5:83641515:C:AC349F0.998
5:83641515:C:GC349S0.998
5:83641516:A:GC349R0.998
5:83641516:A:TC349S0.998
5:83641587:C:GC325S0.998
5:83641588:A:TC325S0.998
5:83641650:C:GC304S0.998
5:83641650:C:TC304Y0.998
5:83641651:A:TC304S0.998
5:83641725:C:AC279F0.998
5:83641725:C:GC279S0.998
5:83641726:A:GC279R0.998
5:83641726:A:TC279S0.998

dbSNP variants (sampled 300 via entrez): RS1000048946 (5:83721143 A>T), RS1000105715 (5:83698402 A>C), RS1000118097 (5:83678053 A>G), RS1000125556 (5:83708968 A>G), RS1000195464 (5:83718538 T>C), RS1000281063 (5:83695715 T>A,C), RS1000286601 (5:83643015 T>C), RS1000364272 (5:83711279 A>G), RS1000411356 (5:83717566 T>C), RS1000443830 (5:83689850 T>A), RS1000456192 (5:83679370 A>G), RS1000544023 (5:83680378 C>T), RS1000558216 (5:83674395 A>G), RS1000560827 (5:83708119 G>A), RS1000600685 (5:83685537 A>C,T)

Disease associations

OMIM: gene MIM:115435 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

14 associations (top):

StudyTraitp-value
GCST000095_3Prostate cancer3.000000e-06
GCST001345_1Ankylosing spondylitis9.000000e-10
GCST001525_14Visceral fat2.000000e-06
GCST002875_12Diisocyanate-induced asthma9.000000e-06
GCST006063_1White matter integrity (fractional anisotropy)5.000000e-10
GCST006064_1White matter integrity (mean diffusivity)6.000000e-13
GCST006585_2705Blood protein levels1.000000e-06
GCST008151_11Waist circumference6.000000e-06
GCST008160_56Waist circumference6.000000e-06
GCST008832_23Gastroesophageal reflux disease2.000000e-08
GCST009391_332Metabolite levels9.000000e-06
GCST009391_358Metabolite levels5.000000e-06
GCST009391_852Metabolite levels8.000000e-06
GCST009921_12Carotid intima media thickness (mean)9.000000e-10

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0006995response to diisocyanate
EFO:0004641white matter integrity
EFO:0010432triacylglycerol 56:5 measurement
EFO:0010434triacylglycerol 56:7 measurement
EFO:0010398sphingomyelin 24:1 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, decreases expression, decreases methylation8
methylmercuric chloridedecreases expression, increases expression3
trichostatin Aaffects cotreatment, increases expression3
mercuric bromideincreases expression, affects cotreatment2
belinostatincreases expression, affects cotreatment2
Vorinostataffects cotreatment, increases expression2
Panobinostataffects cotreatment, increases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Progesteronedecreases expression, increases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, increases expression2
deoxynivalenoldecreases expression1
sodium arsenitedecreases expression1
triadimefondecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Sincreases methylation1
NSC 689534affects binding, decreases expression1
(+)-JQ1 compounddecreases expression1
Sunitinibdecreases expression1
Benzo(a)pyreneincreases methylation, affects methylation1
Copperaffects binding, decreases expression1
Cytarabinedecreases expression1
Diethylhexyl Phthalatedecreases expression, increases expression1
Estradiolaffects expression1
Silicon Dioxideaffects expression1
T-2 Toxindecreases expression1
Tamoxifenaffects expression1
Tretinoinincreases expression1
Triclosandecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): gastroesophageal reflux disease