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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
  • FRAS1-Related Extracellular Matrix Protein 1 3
  • Extracellular Matrix Protein QBRICK 3
  • Chromosome 9 Open Reading Frame 154 2
  • 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. Gene Ontology (GO) annotations related to this gene include calcium ion binding and carbohydrate binding. An important paralog of this gene is FREM2.

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

Additional gene information for FREM1 Gene

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

Genomics for FREM1 Gene

GeneHancer (GH) Regulatory Elements for FREM1 Gene

Promoters and enhancers for FREM1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J014906 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +2.9 2896 5.4 PKNOX1 FOXA2 ZFP64 ARID4B FEZF1 DMAP1 ZNF48 TCF12 GLIS2 ZSCAN16 FREM1 RNU6-1260P LOC389705
GH09J014991 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE 650.2 -81.8 -81803 2.9 HDAC1 ATF1 SIN3A ZBTB40 ETS1 E2F8 EGR1 ATF7 ZBTB11 CEBPB LOC389705 LOC105375980 FREM1 PSIP1P1 CLCN3P1
GH09J014957 Promoter 0.7 EPDnew 650.3 -44.6 -44600 0.1 RCOR1 CHD2 NR2F2 PIR32025 GC09M014957 GC09M014956 GC09M014955 FREM1 LOC105375980
GH09J014934 Enhancer 0.6 ENCODE 15.8 -24.3 -24276 2.6 PKNOX1 ZBTB6 FEZF1 PRDM6 RCOR1 FOXP2 WT1 CHD2 FREM1 LOC389705 LDHAP4 GC09M014957 GC09M014956 GC09M014955 PIR32025
GH09J014888 Enhancer 0.4 ENCODE 18.1 +23.2 23188 0.5 ELF3 HNF1A FOXA2 FREM1 RNU6-1260P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FREM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FREM1 gene promoter:
  • CHOP-10
  • C/EBPalpha
  • c-Myb
  • Pax-6
  • AML1a
  • Lmo2
  • STAT5A
  • NF-1
  • CUTL1

Genomic Locations for FREM1 Gene

Genomic Locations for FREM1 Gene
chr9:14,734,666-14,911,647
(GRCh38/hg38)
Size:
176,982 bases
Orientation:
Minus strand
chr9:14,734,664-14,910,993
(GRCh37/hg19)
Size:
176,330 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

Post-translational modifications for FREM1 Gene

  • Glycosylation at isoforms=21566, Asn1014, isoforms=622, Asn560, and Asn335
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for FREM1 Gene

Domains & Families for FREM1 Gene

Gene Families for FREM1 Gene

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

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.
Domain:
  • The Calx-beta domain binds calcium with high affinity and undergo a major conformational shift upon binding.
Family:
  • Belongs to the FRAS1 family.
genes like me logo Genes that share domains with FREM1: view

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.

Phenotypes From GWAS Catalog for FREM1 Gene

Gene Ontology (GO) - Molecular Function for FREM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030246 carbohydrate binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with FREM1: view
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FREM1

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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
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 FREM1 gene
Compartment Confidence
extracellular 4
plasma membrane 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for FREM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005604 basement membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with FREM1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for FREM1 Gene

Pathways & Interactions for FREM1 Gene

SuperPathways for FREM1 Gene

No Data Available

Interacting Proteins for FREM1 Gene

STRING Interaction Network Preview (showing 2 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000370262%0d%0a9606.ENSP00000264895%0d%0a9606.ENSP00000280481%0d%0a
Selected Interacting proteins: Q5H8C1-FREM1_HUMAN ENSP00000370262 for FREM1 Gene via IID STRING

Gene Ontology (GO) - Biological Process for FREM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007154 cell communication IEA --
GO:0007155 cell adhesion IEA --
GO:0007160 cell-matrix adhesion IEA --
GO:0007275 multicellular organism development IEA --
GO:0097094 craniofacial suture morphogenesis IMP 21931569
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 Approved 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:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FREM1

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for FREM1 Gene



NURSA nuclear receptor signaling pathways regulating expression of FREM1 Gene:

FREM1

SOURCE GeneReport for Unigene cluster for FREM1 Gene:

Hs.50850

Phenotype-based relationships between genes and organs from Gene ORGANizer for FREM1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • lacrimal apparatus
  • lip
  • nose
  • outer ear
  • skull
Abdomen:
  • abdominal wall
  • appendix
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
Pelvis:
  • anus
  • penis
  • rectum
  • vagina
General:
  • hair
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with FREM1: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES 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
chimpanzee
(Pan troglodytes)
Mammalia FREM1 34 33
  • 99.33 (n)
OneToOne
dog
(Canis familiaris)
Mammalia FREM1 34 33
  • 87.05 (n)
OneToOne
cow
(Bos Taurus)
Mammalia FREM1 34 33
  • 86.56 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Frem1 16 34 33
  • 81.88 (n)
rat
(Rattus norvegicus)
Mammalia Frem1 33
  • 81.87 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 80 (a)
OneToMany
-- 34
  • 73 (a)
OneToMany
-- 34
  • 73 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia FREM1 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves FREM1 34 33
  • 70.18 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia FREM1 34
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100488523 33
  • 64.85 (n)
zebrafish
(Danio rerio)
Actinopterygii frem1a 34 33
  • 60.03 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 36 (a)
OneToOne
Species where no ortholog for FREM1 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for FREM1 Gene

ENSEMBL:
Gene Tree for FREM1 (if available)
TreeFam:
Gene Tree for FREM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for FREM1: view image

Paralogs for FREM1 Gene

Paralogs for FREM1 Gene

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

  • FREM1_HUMAN
  • C9JT55_HUMAN
  • F8WE85_HUMAN

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 Variation AA Info Type
rs1032474 benign, not specified, Marles Greenberg Persaud syndrome 14,775,855(-) A/G coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs1041939526 uncertain-significance, Marles Greenberg Persaud syndrome 14,735,838(-) G/C 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1042974040 uncertain-significance, Marles Greenberg Persaud syndrome 14,737,341(-) C/A 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1048070 benign, Marles Greenberg Persaud syndrome 14,735,055(-) T/A/C/G 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1049412089 uncertain-significance, Marles Greenberg Persaud syndrome 14,770,741(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant

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

Variant ID Type Subtype PubMed ID
esv2144591 CNV deletion 18987734
esv2505227 CNV deletion 19546169
esv275116 CNV gain+loss 21479260
esv2761502 CNV loss 21179565
esv3307811 CNV mobile element insertion 20981092
esv3308882 CNV mobile element insertion 20981092
esv3364608 CNV insertion 20981092
esv3388852 CNV insertion 20981092
esv3407326 CNV insertion 20981092
esv3437105 CNV insertion 20981092
esv3891619 CNV loss 25118596
nsv1018416 CNV loss 25217958
nsv1023955 CNV loss 25217958
nsv1125437 OTHER inversion 24896259
nsv1140956 CNV deletion 24896259
nsv1146178 CNV deletion 26484159
nsv416930 CNV deletion 16902084
nsv521718 CNV loss 19592680
nsv613637 CNV gain 21841781
nsv613646 CNV loss 21841781
nsv613647 CNV loss 21841781
nsv6484 CNV insertion 18451855
nsv820261 CNV gain 19587683
nsv831517 CNV loss 17160897
nsv831518 CNV loss 17160897
nsv956120 CNV deletion 24416366

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)

Additional Variant Information for FREM1 Gene

Human Gene Mutation Database (HGMD)
FREM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FREM1

SNP Genotyping and Copy Number Assay Products

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

Disorders for FREM1 Gene

MalaCards: The human disease database

(15) MalaCards diseases for FREM1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
bifid nose with or without anorectal and renal anomalies
  • bnar
manitoba oculotrichoanal syndrome
  • mota
trigonocephaly 2
  • craniosynostosis, metopic
isolated trigonocephaly
  • non-syndromic metopic craniosynostosis
renal hypodysplasia/aplasia 3
  • rhda3
- 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, ECO:0000269 PubMed:28111185}. 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.

Additional Disease Information for FREM1

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

No data available for Genatlas for FREM1 Gene

Publications for FREM1 Gene

  1. Novel FREM1 mutations in a patient with MOTA syndrome: Clinical findings, mutation update and review of FREM1-related disorders literature. (PMID: 28111185) Chacon-Camacho OF … Zenteno JC (European journal of medical genetics 2017) 3 4 58
  2. Heterozygous mutations of FREM1 are associated with an increased risk of isolated metopic craniosynostosis in humans and mice. (PMID: 21931569) Vissers LE … Roscioli T (PLoS genetics 2011) 3 4 58
  3. Manitoba-oculo-tricho-anal (MOTA) syndrome is caused by mutations in FREM1. (PMID: 21507892) Slavotinek AM … Zenker M (Journal of medical genetics 2011) 3 4 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. Identification of 15 loci influencing height in a Korean population. (PMID: 19893584) Kim JJ … Lee JK (Journal of human genetics 2010) 3 44 58

Products for FREM1 Gene

Sources for FREM1 Gene

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