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Aliases for FREM1 Gene

Aliases for FREM1 Gene

  • FRAS1 Related Extracellular Matrix 1 2 3 5
  • C9orf154 3 4
  • C9orf143 3 4
  • C9orf145 3 4
  • Chromosome 9 Open Reading Frame 154 2
  • Extracellular Matrix Protein QBRICK 3
  • Protein QBRICK 4
  • TRIGNO2 3
  • TILRR 3
  • BNAR 3
  • MOTA 3

External Ids for FREM1 Gene

Previous HGNC Symbols for FREM1 Gene

  • C9orf154

Summaries for FREM1 Gene

Entrez Gene Summary for FREM1 Gene

  • This gene encodes a basement membrane protein that may play a role in craniofacial and renal development. Mutations in this gene have been associated with bifid nose with or without anorectal and renal anomalies. Alternatively spliced transcript variants encoding different isoforms have been described. PubMed ID 19940113 describes one such variant that initiates transcription within a distinct, internal exon; the resulting shorter isoform (named Toll-like/interleukin-1 receptor regulator, TILRR) is suggested to be a co-receptor of the interleukin 1 receptor family and may regulate receptor function and Toll-like receptor/interleukin 1 receptor signal transduction, contributing to the control of inflammatory response activation. [provided by RefSeq, Apr 2011]

GeneCards Summary for FREM1 Gene

FREM1 (FRAS1 Related Extracellular Matrix 1) is a Protein Coding gene. Diseases associated with FREM1 include Bifid Nose With Or Without Anorectal And Renal Anomalies and Manitoba Oculotrichoanal Syndrome. GO annotations related to this gene include calcium ion binding and carbohydrate binding. An important paralog of this gene is FREM3.

UniProtKB/Swiss-Prot for FREM1 Gene

  • Extracellular matrix protein that plays a role in epidermal differentiation and is required for epidermal adhesion during embryonic development.

Gene Wiki entry for FREM1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FREM1 Gene

Genomics for FREM1 Gene

Regulatory Elements for FREM1 Gene

Enhancers for FREM1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around FREM1 on UCSC Golden Path with GeneCards custom track

Promoters for FREM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around FREM1 on UCSC Golden Path with GeneCards custom track

Genomic Location for FREM1 Gene

Chromosome:
9
Start:
14,734,666 bp from pter
End:
14,911,647 bp from pter
Size:
176,982 bases
Orientation:
Minus strand

Genomic View for FREM1 Gene

Genes around FREM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FREM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FREM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FREM1 Gene

Proteins for FREM1 Gene

  • Protein details for FREM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5H8C1-FREM1_HUMAN
    Recommended name:
    FRAS1-related extracellular matrix protein 1
    Protein Accession:
    Q5H8C1
    Secondary Accessions:
    • B7ZBX4
    • Q5VV00
    • Q5VV01
    • Q6MZI4
    • Q8NEG9
    • Q96LI3

    Protein attributes for FREM1 Gene

    Size:
    2179 amino acids
    Molecular mass:
    244154 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Was termed QBRICK because it contains 12 repeats: Q stands for queen and is taken from the queen being the 12th in a suit of playing card, and BRICK stands for the repeating unit.
    SequenceCaution:
    • Sequence=AAH31064.2; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAH71826.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for FREM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FREM1 Gene

Proteomics data for FREM1 Gene at MOPED

Post-translational modifications for FREM1 Gene

  • Glycosylation at Asn 335, Asn 560, Asn 622, Asn 1014, and Asn 1566
  • Modification sites at PhosphoSitePlus

Other Protein References for FREM1 Gene

Antibody Products

No data available for DME Specific Peptides for FREM1 Gene

Domains & Families for FREM1 Gene

Protein Domains for FREM1 Gene

Suggested Antigen Peptide Sequences for FREM1 Gene

Graphical View of Domain Structure for InterPro Entry

Q5H8C1

UniProtKB/Swiss-Prot:

FREM1_HUMAN :
  • The Calx-beta domain binds calcium with high affinity and undergo a major conformational shift upon binding.
  • Belongs to the FRAS1 family.
  • Contains 12 CSPG (NG2) repeats.
Domain:
  • The Calx-beta domain binds calcium with high affinity and undergo a major conformational shift upon binding.
  • Contains 1 C-type lectin domain.
  • Contains 1 Calx-beta domain.
Family:
  • Belongs to the FRAS1 family.
Similarity:
  • Contains 12 CSPG (NG2) repeats.
genes like me logo Genes that share domains with FREM1: view

No data available for Gene Families for FREM1 Gene

Function for FREM1 Gene

Molecular function for FREM1 Gene

UniProtKB/Swiss-Prot Function:
Extracellular matrix protein that plays a role in epidermal differentiation and is required for epidermal adhesion during embryonic development.
genes like me logo Genes that share phenotypes with FREM1: view

Human Phenotype Ontology for FREM1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for FREM1 Gene

MGI Knock Outs for FREM1:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for FREM1 Gene

Localization for FREM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FREM1 Gene

Secreted, extracellular space, extracellular matrix, basement membrane. Note=Localizes at the basement membrane zone of embryonic epidermis and hair follicles. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for FREM1 Gene COMPARTMENTS Subcellular localization image for FREM1 gene
Compartment Confidence
extracellular 4
plasma membrane 2
endoplasmic reticulum 1
golgi apparatus 1
lysosome 1
mitochondrion 1
peroxisome 1
vacuole 1

No data available for Gene Ontology (GO) - Cellular Components for FREM1 Gene

Pathways & Interactions for FREM1 Gene

SuperPathways for FREM1 Gene

No Data Available

Interacting Proteins for FREM1 Gene

Selected Interacting proteins: Q5H8C1-FREM1_HUMAN for FREM1 Gene via I2D

Symbol External ID(s) Details
IL1R1
STK3

Gene Ontology (GO) - Biological Process for FREM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007154 cell communication IEA --
genes like me logo Genes that share ontologies with FREM1: view

No data available for Pathways by source and SIGNOR curated interactions for FREM1 Gene

Drugs & Compounds for FREM1 Gene

(1) Drugs for FREM1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with FREM1: view

Transcripts for FREM1 Gene

Unigene Clusters for FREM1 Gene

FRAS1 related extracellular matrix 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for FREM1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b · 16c · 16d
SP1: - - - - -
SP2: - - - - -
SP3: - -
SP4: -
SP5: -

Relevant External Links for FREM1 Gene

GeneLoc Exon Structure for
FREM1
ECgene alternative splicing isoforms for
FREM1

Expression for FREM1 Gene

mRNA expression in normal human tissues for FREM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for FREM1 Gene

This gene is overexpressed in Blymphocyte (25.1), Tlymphocyte (23.4), and Peripheral blood mononuclear cells (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MOPED, and MaxQB for FREM1 Gene



SOURCE GeneReport for Unigene cluster for FREM1 Gene Hs.50850

genes like me logo Genes that share expression patterns with FREM1: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for FREM1 Gene

Orthologs for FREM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for FREM1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia FREM1 35
  • 86.56 (n)
  • 84.03 (a)
FREM1 36
  • 84 (a)
OneToOne
dog
(Canis familiaris)
Mammalia FREM1 35
  • 87.05 (n)
  • 83.79 (a)
FREM1 36
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Frem1 35
  • 81.88 (n)
  • 78.83 (a)
Frem1 16
Frem1 36
  • 78 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia FREM1 35
  • 99.33 (n)
  • 99 (a)
FREM1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Frem1 35
  • 81.87 (n)
  • 78.48 (a)
oppossum
(Monodelphis domestica)
Mammalia FREM1 36
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 73 (a)
OneToMany
-- 36
  • 80 (a)
OneToMany
-- 36
  • 73 (a)
OneToMany
chicken
(Gallus gallus)
Aves FREM1 35
  • 70.18 (n)
  • 67.75 (a)
FREM1 36
  • 67 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia FREM1 36
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100488523 35
  • 64.85 (n)
  • 61.39 (a)
zebrafish
(Danio rerio)
Actinopterygii frem1a 35
  • 60.03 (n)
  • 54.03 (a)
frem1a 36
  • 56 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 36 (a)
OneToOne
Species with no ortholog for FREM1:
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for FREM1 Gene

ENSEMBL:
Gene Tree for FREM1 (if available)
TreeFam:
Gene Tree for FREM1 (if available)

Paralogs for FREM1 Gene

Paralogs for FREM1 Gene

(1) SIMAP similar genes for FREM1 Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for FREM1 Gene

genes like me logo Genes that share paralogs with FREM1: view

Variants for FREM1 Gene

Sequence variations from dbSNP and Humsavar for FREM1 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs2779500 - 14,846,038(-) TTCAG(C/G)TTGTC nc-transcript-variant, reference, missense
rs1353223 - 14,842,559(+) AAATA(C/T)CCGGA nc-transcript-variant, reference, missense
rs7023244 - 14,819,372(+) CATCA(G/T)AAATT nc-transcript-variant, reference, missense
rs7041710 - 14,816,831(+) CAAGA(C/G)TAGGT nc-transcript-variant, reference, missense
rs16932300 - 14,801,740(+) TCTTT(C/G)CTAAA nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for FREM1 Gene

Variant ID Type Subtype PubMed ID
nsv831517 CNV Loss 17160897
nsv892614 CNV Gain 21882294
nsv831518 CNV Loss 17160897
dgv8110n71 CNV Gain 21882294
nsv416930 CNV Loss 16902084
nsv892617 CNV Gain 21882294
nsv892618 CNV Loss 21882294
nsv6484 CNV Insertion 18451855
nsv892619 CNV Gain 21882294
esv2505227 CNV Deletion 19546169
esv2144591 CNV Deletion 18987734
nsv521718 CNV Loss 19592680
nsv820261 CNV Gain 19587683
esv272085 CNV Insertion 20981092
esv273155 CNV Insertion 20981092
esv275116 CNV Gain+Loss 21479260
esv274583 CNV Insertion 20981092

Variation tolerance for FREM1 Gene

Residual Variation Intolerance Score: 72.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.32; 96.30% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for FREM1 Gene

Human Gene Mutation Database (HGMD)
FREM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FREM1 Gene

Disorders for FREM1 Gene

MalaCards: The human disease database

(19) MalaCards diseases for FREM1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
bifid nose with or without anorectal and renal anomalies
  • bnar syndrome
manitoba oculotrichoanal syndrome
  • marles syndrome
trigonocephaly 2
  • metopic craniosynostosis
isolated trigonocephaly
  • non-syndromic metopic craniosynostosis
trigonocephaly 1
  • trigonocephaly 2
- elite association - COSMIC cancer census association via MalaCards
Search FREM1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

FREM1_HUMAN
  • Bifid nose, with or without anorectal and renal anomalies (BNAR) [MIM:608980]: A disease characterized by the presence of a bifid nose usually associated with renal agenesis and anorectal malformations. A bifid nose is a congenital deformity due to failure of the paired nasal processes to fuse to a single midline organ during early gestation. {ECO:0000269 PubMed:19732862}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Manitoba oculotrichoanal syndrome (MOTA) [MIM:248450]: A rare condition defined by eyelid colobomas, cryptophthalmos, and anophthalmia/microphthalmia, an aberrant hairline, a bifid or broad nasal tip, and gastrointestinal anomalies such as omphalocele and anal stenosis. {ECO:0000269 PubMed:21507892}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Trigonocephaly 2 (TRIGNO2) [MIM:614485]: A keel-shaped deformation of the forehead, caused by premature fusion of the metopic sutures. It results in a triangular shape of the head. {ECO:0000269 PubMed:21931569}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for FREM1

Genetic Association Database (GAD)
FREM1
Human Genome Epidemiology (HuGE) Navigator
FREM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
FREM1
genes like me logo Genes that share disorders with FREM1: view

No data available for Genatlas for FREM1 Gene

Publications for FREM1 Gene

  1. Manitoba-oculo-tricho-anal (MOTA) syndrome is caused by mutations in FREM1. (PMID: 21507892) Slavotinek A.M. … Zenker M. (J. Med. Genet. 2011) 3 4 67
  2. The extracellular matrix gene Frem1 is essential for the normal adhesion of the embryonic epidermis. (PMID: 15345741) Smyth I. … Jackson I.J. (Proc. Natl. Acad. Sci. U.S.A. 2004) 2 3
  3. Human and mouse proteases: a comparative genomic approach. (PMID: 12838346) Puente X.S. … Lopez-Otin C. (Nat. Rev. Genet. 2003) 2 3
  4. Mild recessive mutations in six Fraser syndrome-related genes cause isolated congenital anomalies of the kidney and urinary tract. (PMID: 24700879) Kohl S. … Hildebrandt F. (J. Am. Soc. Nephrol. 2014) 3
  5. Deficiency of FRAS1-related extracellular matrix 1 (FREM1) causes congenital diaphragmatic hernia in humans and mice. (PMID: 23221805) Beck T.F. … Scott D.A. (Hum. Mol. Genet. 2013) 3

Products for FREM1 Gene

Sources for FREM1 Gene

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