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Aliases for FREM3 Gene

Aliases for FREM3 Gene

  • FRAS1 Related Extracellular Matrix 3 2 3 5
  • FRAS1-Related Extracellular Matrix Protein 3 3

External Ids for FREM3 Gene

Previous GeneCards Identifiers for FREM3 Gene

  • GC04M144849
  • GC04M144717
  • GC04M144498
  • GC04M140228

Summaries for FREM3 Gene

Entrez Gene Summary for FREM3 Gene

  • This gene encodes an integral membrane protein containing numerous CSPG (chondroitin sulfate proteoglycan element) repeats and Calx-beta domains. The protein belongs to the family of FRAS1/FREM extracellular matrix proteins and may play a role cell adhesion. [provided by RefSeq, Feb 2017]

GeneCards Summary for FREM3 Gene

FREM3 (FRAS1 Related Extracellular Matrix 3) is a Protein Coding gene. Diseases associated with FREM3 include Fraser Syndrome 1 and Renal Hypodysplasia/Aplasia 1. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is FREM2.

UniProtKB/Swiss-Prot for FREM3 Gene

  • Extracellular matrix protein which may play a role in cell adhesion.

Additional gene information for FREM3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FREM3 Gene

Genomics for FREM3 Gene

GeneHancer (GH) Regulatory Elements for FREM3 Gene

Promoters and enhancers for FREM3 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
GH04J143700 Enhancer 0.4 Ensembl 650.7 -0.3 -326 0.4 SUZ12 REST EZH2 FREM3 LOC100419356 ENSG00000251600
GH04J143905 Promoter 1.2 EPDnew 10.9 -204.9 -204904 0.1 PKNOX1 ATF1 ARNT NCOA2 TCF12 ATF7 NCOA1 REST ZNF592 ATF4 GYPE FREM3 LOC100420464 ENSG00000251600
GH04J143558 Promoter/Enhancer 1.3 Ensembl ENCODE 10 +141.4 141373 1.5 PKNOX1 ARID4B SIN3A ZNF48 RAD21 YY1 TCF12 ZNF143 RUNX3 CREM GUSBP5 ENSG00000251600 FREM3 ENSG00000248924
GH04J143910 Promoter/Enhancer 1.1 Ensembl ENCODE 10.9 -210.9 -210926 2 SMARCA5 ZNF687 L3MBTL2 BACH1 MEF2B ELF1 POLR2A GABPB1 IKZF1 ETV6 LOC101927636 LOC100420464 LOC100419356 FREM3 GYPE ENSG00000251600
GH04J143774 Enhancer 0.8 ENCODE 11 -73.5 -73478 0.1 HDGF ATF1 RB1 ZNF2 RAD21 CHAMP1 E2F8 ARID2 ZNF143 ATF7 FREM3 LOC100419356 LOC105377458 ENSG00000251600
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around FREM3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FREM3 gene promoter:

Genomic Locations for FREM3 Gene

Genomic Locations for FREM3 Gene
123,374 bases
Minus strand

Genomic View for FREM3 Gene

Genes around FREM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FREM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FREM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FREM3 Gene

Proteins for FREM3 Gene

  • Protein details for FREM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    FRAS1-related extracellular matrix protein 3
    Protein Accession:

    Protein attributes for FREM3 Gene

    2139 amino acids
    Molecular mass:
    238179 Da
    Quaternary structure:
    No Data Available

neXtProt entry for FREM3 Gene

Post-translational modifications for FREM3 Gene

  • Glycosylation at Asn1588, isoforms=1374, isoforms=1368, and Asn846
  • Modification sites at PhosphoSitePlus

Other Protein References for FREM3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FREM3 Gene

Domains & Families for FREM3 Gene

Gene Families for FREM3 Gene

Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for FREM3 Gene

Suggested Antigen Peptide Sequences for FREM3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The Calx-beta domains bind calcium with high affinity and undergo a major conformational shift upon binding.
  • Belongs to the FRAS1 family.
  • The Calx-beta domains bind calcium with high affinity and undergo a major conformational shift upon binding.
  • Belongs to the FRAS1 family.
genes like me logo Genes that share domains with FREM3: view

Function for FREM3 Gene

Molecular function for FREM3 Gene

UniProtKB/Swiss-Prot Function:
Extracellular matrix protein which may play a role in cell adhesion.

Phenotypes From GWAS Catalog for FREM3 Gene

Gene Ontology (GO) - Molecular Function for FREM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with FREM3: view

Phenotypes for FREM3 Gene

genes like me logo Genes that share phenotypes with FREM3: view

Animal Model Products

CRISPR Products

miRNA for FREM3 Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FREM3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for FREM3 Gene

Localization for FREM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FREM3 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 FREM3 gene
Compartment Confidence
extracellular 5
plasma membrane 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for FREM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005604 basement membrane ISS --
GO:0005615 extracellular space HDA 22664934
GO:0016021 integral component of membrane IEA --
GO:0031012 colocalizes_with extracellular matrix TAS 22261194
genes like me logo Genes that share ontologies with FREM3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for FREM3 Gene

Pathways & Interactions for FREM3 Gene

SuperPathways for FREM3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for FREM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007154 cell communication IEA --
GO:0007155 cell adhesion NAS 18661360
genes like me logo Genes that share ontologies with FREM3: view

No data available for Pathways by source and SIGNOR curated interactions for FREM3 Gene

Drugs & Compounds for FREM3 Gene

(1) Drugs for FREM3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with FREM3: view

Transcripts for FREM3 Gene

mRNA/cDNA for FREM3 Gene

(10) Selected AceView cDNA sequences:
(0) Additional mRNA sequences :
(1) REFSEQ mRNAs :
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for FREM3 Gene

FRAS1 related extracellular matrix 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FREM3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for FREM3 Gene

No ASD Table

Relevant External Links for FREM3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for FREM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FREM3 Gene

mRNA differential expression in normal tissues according to GTEx for FREM3 Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (x13.8), Brain - Cortex (x13.0), and Brain - Frontal Cortex (BA9) (x12.5).

Protein differential expression in normal tissues from HIPED for FREM3 Gene

This gene is overexpressed in Gallbladder (28.3), Nasopharynx (9.9), Urinary Bladder (6.5), and Adrenal (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for FREM3 Gene

NURSA nuclear receptor signaling pathways regulating expression of FREM3 Gene:


SOURCE GeneReport for Unigene cluster for FREM3 Gene:

genes like me logo Genes that share expression patterns with FREM3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for FREM3 Gene

Orthologs for FREM3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for FREM3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia FREM3 34 33
  • 99.25 (n)
(Canis familiaris)
Mammalia FREM3 33
  • 82.8 (n)
-- 34
  • 17 (a)
(Bos Taurus)
Mammalia FREM3 33
  • 82.25 (n)
-- 34
  • 15 (a)
(Mus musculus)
Mammalia Frem3 16 34 33
  • 76.96 (n)
(Rattus norvegicus)
Mammalia Frem3 33
  • 76.69 (n)
(Monodelphis domestica)
Mammalia FREM3 34
  • 45 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 13 (a)
(Gallus gallus)
Aves -- 34
  • 15 (a)
(Anolis carolinensis)
Reptilia FREM3 34
  • 42 (a)
(Danio rerio)
Actinopterygii frem3 34
  • 40 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 33 (a)
Species where no ortholog for FREM3 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 FREM3 Gene

Gene Tree for FREM3 (if available)
Gene Tree for FREM3 (if available)
Evolutionary constrained regions (ECRs) for FREM3: view image

Paralogs for FREM3 Gene

Paralogs for FREM3 Gene

(2) SIMAP similar genes for FREM3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with FREM3: view

Variants for FREM3 Gene

Sequence variations from dbSNP and Humsavar for FREM3 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1057518624 uncertain-significance, not specified 143,700,585(-) CCTGCAGCGC/C coding_sequence_variant, inframe_deletion
rs886043245 uncertain-significance, not specified 143,621,088(-) G/A/T coding_sequence_variant, stop_gained, synonymous_variant
rs1000023954 -- 143,681,647(-) A/G intron_variant
rs1000065034 -- 143,682,366(-) A/C/G intron_variant
rs1000074296 -- 143,690,531(-) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for FREM3 Gene

Variant ID Type Subtype PubMed ID
esv2669991 CNV deletion 23128226
esv2728475 CNV deletion 23290073
esv2759288 CNV gain+loss 17122850
esv3564747 CNV deletion 23714750
esv3602511 CNV loss 21293372
esv3894047 CNV gain 25118596
esv4609 CNV loss 18987735
esv9197 CNV loss 19470904
nsv1114576 CNV deletion 24896259
nsv1161158 CNV duplication 26073780
nsv293188 CNV deletion 16902084
nsv428452 CNV loss 18775914
nsv4533 CNV insertion 18451855
nsv830103 CNV loss 17160897
nsv956927 CNV deletion 24416366

Variation tolerance for FREM3 Gene

Gene Damage Index Score: 9.92; 89.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FREM3 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 FREM3 Gene

Disorders for FREM3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for FREM3 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
fraser syndrome 1
  • frasrs1
renal hypodysplasia/aplasia 1
  • rhda1
- elite association - COSMIC cancer census association via MalaCards
Search FREM3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for FREM3

genes like me logo Genes that share disorders with FREM3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for FREM3 Gene

Publications for FREM3 Gene

  1. The extracellular matrix gene Frem1 is essential for the normal adhesion of the embryonic epidermis. (PMID: 15345741) Smyth I … Jackson IJ (Proceedings of the National Academy of Sciences of the United States of America 2004) 2 3 4 58
  2. The Fras1/Frem family of extracellular matrix proteins: structure, function, and association with Fraser syndrome and the mouse bleb phenotype. (PMID: 18661360) Petrou P … Chalepakis G (Connective tissue research 2008) 3 22 58
  3. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 58
  4. FRAS1-related extracellular matrix 3 (FREM3) single-nucleotide polymorphism effects on gene expression, amygdala reactivity and perceptual processing speed: An accelerated aging pathway of depression risk. (PMID: 26441752) Nikolova YS … Sibille E (Frontiers in psychology 2015) 3 58
  5. Proteomics analysis of cardiac extracellular matrix remodeling in a porcine model of ischemia/reperfusion injury. (PMID: 22261194) Barallobre-Barreiro J … Mayr M (Circulation 2012) 3 58

Products for FREM3 Gene

Sources for FREM3 Gene

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