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Aliases for MATN3 Gene

Aliases for MATN3 Gene

  • Matrilin 3 2 3 5
  • Matrilin-3 3
  • DIPOA 3
  • OADIP 3
  • EDM5 3
  • HOA 3
  • OS2 3

External Ids for MATN3 Gene

Previous GeneCards Identifiers for MATN3 Gene

  • GC02M020083
  • GC02M020259
  • GC02M020176
  • GC02M020113
  • GC02M019949
  • GC02M020191

Summaries for MATN3 Gene

Entrez Gene Summary for MATN3 Gene

  • This gene encodes a member of von Willebrand factor A domain containing protein family. This family of proteins is thought to be involved in the formation of filamentous networks in the extracellular matrices of various tissues. This protein contains two von Willebrand factor A domains; it is present in the cartilage extracellular matrix and has a role in the development and homeostasis of cartilage and bone. Mutations in this gene result in multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]

GeneCards Summary for MATN3 Gene

MATN3 (Matrilin 3) is a Protein Coding gene. Diseases associated with MATN3 include Spondyloepimetaphyseal Dysplasia, Matrilin-3 Related and Epiphyseal Dysplasia, Multiple, 5. Among its related pathways are ECM proteoglycans and Degradation of the extracellular matrix. Gene Ontology (GO) annotations related to this gene include calcium ion binding and extracellular matrix structural constituent. An important paralog of this gene is MATN2.

UniProtKB/Swiss-Prot for MATN3 Gene

  • Major component of the extracellular matrix of cartilage and may play a role in the formation of extracellular filamentous networks.

Gene Wiki entry for MATN3 Gene

Additional gene information for MATN3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MATN3 Gene

Genomics for MATN3 Gene

GeneHancer (GH) Regulatory Elements for MATN3 Gene

Promoters and enhancers for MATN3 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
GH02J020011 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 662 +0.0 6 2.8 ELF3 FOXA2 ARID4B SIN3A DNMT3B ZNF48 RARA SLC30A9 RCOR1 CREM MATN3 TTC32 LOC101928222
GH02J020047 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 18.2 -38.1 -38057 5.5 MLX ZFP64 FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC LOC105373463 LAPTM4A MATN3 ENSG00000234378 TTC32 PUM2 PIR35445 GC02P020023
GH02J020090 Enhancer 1.4 Ensembl ENCODE dbSUPER 25.9 -80.3 -80318 4.9 FOXA2 MLX ARID4B DMAP1 ZNF48 ETS1 SLC30A9 TCF12 GATA2 ZFP91 GC02M020086 MATN3 ENSG00000234378 LOC101928222 WDR35 RNU6-961P RNU7-113P LOC105373463
GH02J020061 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 26.9 -50.3 -50337 3.4 SP3 ZNF362 SP2 ZNF384 MEF2B CC2D1A ZSCAN21 ZNF335 ATF7 FOS MATN3 LOC105373463 TTC32 GC02M020086 ENSG00000234378
GH02J019899 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 15 +111.1 111083 3.6 CLOCK DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 SSRP1 ZNF610 TTC32 ENSG00000271991 PUM2 MATN3 LINC00954 WDR35
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MATN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the MATN3 gene promoter:
  • AREB6
  • POU2F1a
  • POU2F1
  • FAC1
  • AML1a
  • NF-1
  • YY1
  • c-Myb
  • ATF6

Genomic Locations for MATN3 Gene

Genomic Locations for MATN3 Gene
20,643 bases
Minus strand
20,643 bases
Minus strand

Genomic View for MATN3 Gene

Genes around MATN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MATN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MATN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MATN3 Gene

Proteins for MATN3 Gene

  • Protein details for MATN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2CPU0
    • Q4ZG02

    Protein attributes for MATN3 Gene

    486 amino acids
    Molecular mass:
    52817 Da
    Quaternary structure:
    • Can form homooligomers (monomers, dimers, trimers and tetramers) and heterooligomers with matrilin-1 (By similarity). Interacts with COMP.

    Alternative splice isoforms for MATN3 Gene


neXtProt entry for MATN3 Gene

Post-translational modifications for MATN3 Gene

  • Glycosylation at posLast=6565 and isoforms=253
  • Modification sites at PhosphoSitePlus

Other Protein References for MATN3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for MATN3 Gene

Domains & Families for MATN3 Gene

Gene Families for MATN3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for MATN3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with MATN3: view

No data available for UniProtKB/Swiss-Prot for MATN3 Gene

Function for MATN3 Gene

Molecular function for MATN3 Gene

UniProtKB/Swiss-Prot Function:
Major component of the extracellular matrix of cartilage and may play a role in the formation of extracellular filamentous networks.
GENATLAS Biochemistry:
matrilin 3,involved in the differentiation state of chondrocytes

Phenotypes From GWAS Catalog for MATN3 Gene

Gene Ontology (GO) - Molecular Function for MATN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent TAS 9350998
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 15075323
genes like me logo Genes that share ontologies with MATN3: view
genes like me logo Genes that share phenotypes with MATN3: view

Human Phenotype Ontology for MATN3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for MATN3 Gene

MGI Knock Outs for MATN3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MATN3

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for MATN3 Gene

Localization for MATN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MATN3 Gene


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 MATN3 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
plasma membrane 1
peroxisome 1
nucleus 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for MATN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with MATN3: view

Pathways & Interactions for MATN3 Gene

genes like me logo Genes that share pathways with MATN3: view

Pathways by source for MATN3 Gene

2 Reactome pathways for MATN3 Gene

Gene Ontology (GO) - Biological Process for MATN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 9350998
GO:0030198 extracellular matrix organization TAS --
GO:0043687 post-translational protein modification TAS --
GO:0044267 cellular protein metabolic process TAS --
genes like me logo Genes that share ontologies with MATN3: view

No data available for SIGNOR curated interactions for MATN3 Gene

Drugs & Compounds for MATN3 Gene

(1) Drugs for MATN3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with MATN3: view

Transcripts for MATN3 Gene

mRNA/cDNA for MATN3 Gene

(1) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(48) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for MATN3 Gene

Matrilin 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MATN3

Alternative Splicing Database (ASD) splice patterns (SP) for MATN3 Gene

No ASD Table

Relevant External Links for MATN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MATN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MATN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for MATN3 Gene

This gene is overexpressed in Nerve - Tibial (x5.0).

Protein differential expression in normal tissues from HIPED for MATN3 Gene

This gene is overexpressed in Liver (41.1) and Breast (27.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for MATN3 Gene

Protein tissue co-expression partners for MATN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of MATN3 Gene:


SOURCE GeneReport for Unigene cluster for MATN3 Gene:


mRNA Expression by UniProt/SwissProt for MATN3 Gene:

Tissue specificity: Expressed only in cartilaginous tissues, such as vertebrae, ribs and shoulders.

Phenotype-based relationships between genes and organs from Gene ORGANizer for MATN3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • immune
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • peripheral nerve
  • peripheral nervous system
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with MATN3: view

No data available for Evidence on tissue expression from TISSUES for MATN3 Gene

Orthologs for MATN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for MATN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia MATN3 34 33
  • 99.11 (n)
(Canis familiaris)
Mammalia MATN3 34 33
  • 86.56 (n)
(Bos Taurus)
Mammalia MATN3 34 33
  • 86.07 (n)
(Mus musculus)
Mammalia Matn3 16 34 33
  • 83.52 (n)
(Rattus norvegicus)
Mammalia Matn3 33
  • 82.26 (n)
(Gallus gallus)
Aves MATN3 34 33
  • 65.52 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia matn3 33
  • 65.31 (n)
(Danio rerio)
Actinopterygii matn3a 34
  • 50 (a)
matn3b 34
  • 39 (a)
(Caenorhabditis elegans)
Secernentea mup-4 34
  • 7 (a)
Species where no ortholog for MATN3 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • wheat (Triticum aestivum)

Evolution for MATN3 Gene

Gene Tree for MATN3 (if available)
Gene Tree for MATN3 (if available)
Evolutionary constrained regions (ECRs) for MATN3: view image

Paralogs for MATN3 Gene

Paralogs for MATN3 Gene

(4) SIMAP similar genes for MATN3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with MATN3: view

Variants for MATN3 Gene

Sequence variations from dbSNP and Humsavar for MATN3 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs104893637 pathogenic, Multiple epiphyseal dysplasia 5, Multiple epiphyseal dysplasia 5 (EDM5) [MIM:607078] 20,006,173(-) G/A coding_sequence_variant, missense_variant
rs104893639 pathogenic, Spondyloepimetaphyseal dysplasia Matrilin-3 related, Spondyloepimetaphyseal dysplasia MATN3-related (SEMD-MATN3) [MIM:608728] 20,003,167(-) A/T coding_sequence_variant, missense_variant
rs104893640 pathogenic, Multiple epiphyseal dysplasia 5, Multiple Epiphyseal Dysplasia, Dominant, Multiple epiphyseal dysplasia 5 (EDM5) [MIM:607078] 20,012,423(-) C/T coding_sequence_variant, missense_variant
rs104893641 pathogenic, Multiple epiphyseal dysplasia 5, Multiple epiphyseal dysplasia 5 (EDM5) [MIM:607078] 20,006,152(-) C/G coding_sequence_variant, missense_variant
rs104893645 pathogenic, Multiple epiphyseal dysplasia 5, Multiple epiphyseal dysplasia 5 (EDM5) [MIM:607078] 20,005,953(-) A/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for MATN3 Gene

Variant ID Type Subtype PubMed ID
dgv3736n100 CNV gain 25217958
esv29979 CNV loss 17803354

Variation tolerance for MATN3 Gene

Residual Variation Intolerance Score: 84.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.93; 59.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MATN3 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MATN3 Gene

Disorders for MATN3 Gene

MalaCards: The human disease database

(12) MalaCards diseases for MATN3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search MATN3 in MalaCards View complete list of genes associated with diseases


  • Multiple epiphyseal dysplasia 5 (EDM5) [MIM:607078]: A generalized skeletal dysplasia associated with significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. Radiological examination of the skeleton shows delayed, irregular mineralization of the epiphyseal ossification centers and of the centers of the carpal and tarsal bones. Multiple epiphyseal dysplasia is broadly categorized into the more severe Fairbank and the milder Ribbing types. The Fairbank type is characterized by shortness of stature, short and stubby fingers, small epiphyses in several joints, including the knee, ankle, hand, and hip. The Ribbing type is confined predominantly to the hip joints and is characterized by hands that are normal and stature that is normal or near-normal. Multiple epiphyseal dysplasia type 5 is relatively mild and clinically variable. It is primarily characterized by delayed and irregular ossification of the epiphyses and early-onset osteoarthritis. {ECO:0000269 PubMed:11479597, ECO:0000269 PubMed:12884427, ECO:0000269 PubMed:14729835, ECO:0000269 PubMed:15459972, ECO:0000269 PubMed:15948199, ECO:0000269 PubMed:16287128, ECO:0000269 PubMed:21922596}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Spondyloepimetaphyseal dysplasia MATN3-related (SEMD-MATN3) [MIM:608728]: A bone disease characterized by disproportionate early-onset dwarfism, bowing of the lower limbs, lumbar lordosis and normal hands. Skeletal abnormalities include short, wide and stocky long bones with severe epiphyseal and metaphyseal changes, hypoplastic iliac bones and flat, ovoid vertebral bodies. {ECO:0000269 PubMed:15121775}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Osteoarthritis 2 (OS2) [MIM:140600]: A degenerative disease of the joints characterized by degradation of the hyaline articular cartilage and remodeling of the subchondral bone with sclerosis. Clinical symptoms include pain and joint stiffness often leading to significant disability and joint replacement. In the hand, osteoarthritis can develop in the distal interphalangeal and the first carpometacarpal (base of thumb) and proximal interphalangeal joints. Patients with osteoarthritis may have one, a few, or all of these sites affected. {ECO:0000269 PubMed:12736871}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Additional Disease Information for MATN3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with MATN3: view

No data available for Genatlas for MATN3 Gene

Publications for MATN3 Gene

  1. Mutations in the region encoding the von Willebrand factor A domain of matrilin-3 are associated with multiple epiphyseal dysplasia. (PMID: 11479597) Chapman KL … Briggs MD (Nature genetics 2001) 3 4 22 44 58
  2. Primary structure of matrilin-3, a new member of a family of extracellular matrix proteins related to cartilage matrix protein (matrilin-1) and von Willebrand factor. (PMID: 9287130) Wagener R … Paulsson M (FEBS letters 1997) 2 3 4 22 58
  3. Mutations in the known genes are not the major cause of MED; distinctive phenotypic entities among patients with no identified mutations. (PMID: 15523498) Jakkula E … Ala-Kokko L (European journal of human genetics : EJHG 2005) 3 22 44 58
  4. Multiple epiphyseal dysplasia mutations in MATN3 cause misfolding of the A-domain and prevent secretion of mutant matrilin-3. (PMID: 16287128) Cotterill SL … Briggs MD (Human mutation 2005) 3 4 22 58
  5. Interactions between the cartilage oligomeric matrix protein and matrilins. Implications for matrix assembly and the pathogenesis of chondrodysplasias. (PMID: 15075323) Mann HH … Wagener R (The Journal of biological chemistry 2004) 3 4 22 58

Products for MATN3 Gene

Sources for MATN3 Gene

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