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    FRAS1 Fraser extracellular matrix complex subunit 1 [ Homo sapiens (human) ]

    Gene ID: 80144, updated on 5-Mar-2024

    Summary

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    Official Symbol
    FRAS1provided by HGNC
    Official Full Name
    Fraser extracellular matrix complex subunit 1provided by HGNC
    Primary source
    HGNC:HGNC:19185
    See related
    Ensembl:ENSG00000138759 MIM:607830; AllianceGenome:HGNC:19185
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    FRASRS1
    Summary
    This gene encodes an extracellular matrix protein that appears to function in the regulation of epidermal-basement membrane adhesion and organogenesis during development. Mutations in this gene cause Fraser syndrome, a multisystem malformation that can include craniofacial, urogenital and respiratory system abnormalities. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
    Expression
    Broad expression in thyroid (RPKM 6.8), kidney (RPKM 4.0) and 15 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    4q21.21
    Exon count:
    74
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (78057323..78544269)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (81398139..81879833)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (78978477..79465423)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:78904281-78905096 Neighboring gene high mobility group box 1 pseudogene 44 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 56 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:78977063-78978034 Neighboring gene uncharacterized LOC107986293 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:79013872-79014616 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:79026548-79027162 Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 5 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:79143534-79144418 Neighboring gene Sharpr-MPRA regulatory region 11576 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:79228222-79228817 Neighboring gene small nucleolar RNA, C/D box 161 Neighboring gene MICOS10 pseudogene 4 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:79402250-79403449 Neighboring gene Sharpr-MPRA regulatory region 1185 Neighboring gene Sharpr-MPRA regulatory region 14158 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:79455131-79456330 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:79473344-79474543 Neighboring gene uncharacterized LOC124900721 Neighboring gene annexin A3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. A polymorphism in the promoter of FRAS1 is a candidate SNP associated with metastatic prostate cancer. Wang V, et al. Prostate, 2021 Jul. PMID 33956343, Free PMC Article
    2. Two unrelated families with variable expression of Fraser syndrome due to the same pathogenic variant in the FRAS1 gene. Midro AT, et al. Am J Med Genet A, 2020 Apr. PMID 31999076
    3. Fraser extracellular matrix complex subunit 1 promotes liver metastasis of gastric cancer. Umeda S, et al. Int J Cancer, 2020 May 15. PMID 31597194
    4. Expanding the mutation spectrum for Fraser syndrome: identification of a novel heterozygous deletion in FRAS1. Hoefele J, et al. Gene, 2013 May 15. PMID 23473829
    5. Clinical and molecular studies in two families with Fraser syndrome: a new FRAS1 gene mutation, prenatal ultrasound findings and implications for genetic counselling. Ogur G, et al. Genet Couns, 2011. PMID 22029163

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A polymorphism in the promoter of FRAS1 is a candidate SNP associated with metastatic prostate cancer.
      Title: A polymorphism in the promoter of FRAS1 is a candidate SNP associated with metastatic prostate cancer.
    2. Novel loss of function variants in FRAS1 AND FREM2 underlie renal agenesis in consanguineous families.
      Title: Novel loss of function variants in FRAS1 AND FREM2 underlie renal agenesis in consanguineous families.
    3. Two unrelated families with variable expression of Fraser syndrome due to the same pathogenic variant in the FRAS1 gene.
      Title: Two unrelated families with variable expression of Fraser syndrome due to the same pathogenic variant in the FRAS1 gene.
    4. Fraser extracellular matrix complex subunit 1 promotes liver metastasis of gastric cancer.
      Title: Fraser extracellular matrix complex subunit 1 promotes liver metastasis of gastric cancer.
    5. Based on these data, we conclude that deficiency of FREM2, and possibly FRAS1, are associated with an increased risk of developing Congenital diaphragmatic hernia (CDH) and that loss of the FREM1/FREM2/FRAS1 complex, or its function, leads to anterior sac CDH development through its effects on mesothelial fold progression
      Title: The role of FREM2 and FRAS1 in the development of congenital diaphragmatic hernia.
    6. In 15 of 590 families, we identified recessive mutations in the genes FRAS1, FREM2, GRIP1, FREM1, ITGA8, and GREM1, all of which function in the interaction of the ureteric bud and the metanephric mesenchyme.
      Title: Mild recessive mutations in six Fraser syndrome-related genes cause isolated congenital anomalies of the kidney and urinary tract.
    7. Analysis of FRAS1 and STRA6 mutations in the same family with eye anomalies.
      Title: A puzzle over several decades: eye anomalies with FRAS1 and STRA6 mutations in the same family.
    8. First case of a family with two patients affected by Fraser syndrome due to a deletion of 64 kb (deletion 4q21.21) and an additional novel frameshift mutation in exon 66 of the FRAS1 gene.
      Title: Expanding the mutation spectrum for Fraser syndrome: identification of a novel heterozygous deletion in FRAS1.
    9. Heterozygous missense mutations in FRAS1 cause non-syndromic congenital abnormalities of the kidney and urinary tract in humans.
      Title: Identification of two novel CAKUT-causing genes by massively parallel exon resequencing of candidate genes in patients with unilateral renal agenesis.
    10. molecular, clinical findings of 4 fetuses with Fraser syndrome from 2 families; in family one, found nonsense mutation (c.3730C>T, p.R1244X) previously described; in family 2 found a novel nonsense mutation previously not known (c.370C>T, p.R124X)
      Title: Clinical and molecular studies in two families with Fraser syndrome: a new FRAS1 gene mutation, prenatal ultrasound findings and implications for genetic counselling.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Fraser syndrome 1
    MedGen: C4551480 OMIM: 219000 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome wide association study of plasma uric acid levels in obese cases and never-overweight controls.
    EBI GWAS Catalog
    Common variants in the trichohyalin gene are associated with straight hair in Europeans.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ14927, FLJ22031, KIAA1500, DKFZp686I05113, DKFZp686P08111

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in anatomical structure morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell communication IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in embryonic limb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in metanephros morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in morphogenesis of an epithelium IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in roof of mouth development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in skin development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in basement membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    extracellular matrix organizing protein FRAS1
    Names
    Fraser syndrome 1
    extracellular matrix protein FRAS1
    fraser syndrome 1 protein

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_015812.2 RefSeqGene

      Range
      4754..491700
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001166133.2 → NP_001159605.1  extracellular matrix organizing protein FRAS1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001159605.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the presence and absence of exons in its 3' coding region and 3' UTR, compared to variant 1, resulting in an isoform (2) with a distinct and significantly shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      AC093652, AC093886, AK025684, BC131820, DA725113, DA881824
      Consensus CDS
      CCDS54772.1
      UniProtKB/TrEMBL
      A0A804HI32
      Related
      ENSP00000326330.6, ENST00000325942.11
      Conserved Domains (8) summary
      smart00214
      Location:367 → 416
      VWC; von Willebrand factor (vWF) type C domain
      smart00261
      Location:952 → 996
      FU; Furin-like repeats
      cd00064
      Location:608 → 653
      FU; Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
      pfam00093
      Location:95 → 152
      VWC; von Willebrand factor type C domain
      pfam14843
      Location:512 → 623
      GF_recep_IV; Growth factor receptor domain IV
      pfam15913
      Location:1009 → 1099
      Furin-like_2; Furin-like repeat, cysteine-rich
      pfam16184
      Location:1168 → 1310
      Cadherin_3; Cadherin-like
      cl17735
      Location:159 → 216
      VWC; von Willebrand factor type C domain

    2. NM_025074.7 → NP_079350.5  extracellular matrix organizing protein FRAS1 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB040933, AC093652, AC093886, AC104808, BC131820, BX647420, BX647949, DA725113, DA881824
      Consensus CDS
      CCDS54771.1
      UniProtKB/Swiss-Prot
      A2RRR8, Q86UZ4, Q86XX4, Q8N3U9, Q8NAU7, Q96JW7, Q9H6N9, Q9P228
      Related
      ENSP00000422834.2, ENST00000512123.4
      Conserved Domains (10) summary
      smart00237
      Location:2555 → 2650
      Calx_beta; Domains in Na-Ca exchangers and integrin-beta4
      smart00214
      Location:367 → 416
      VWC; von Willebrand factor (vWF) type C domain
      smart00261
      Location:952 → 996
      FU; Furin-like repeats
      cd00064
      Location:608 → 653
      FU; Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
      pfam00093
      Location:95 → 152
      VWC; von Willebrand factor type C domain
      pfam00757
      Location:462 → 620
      Furin-like; Furin-like cysteine rich region
      pfam14843
      Location:655 → 777
      GF_recep_IV; Growth factor receptor domain IV
      pfam15913
      Location:1009 → 1099
      Furin-like_2; Furin-like repeat, cysteine-rich
      pfam16184
      Location:2261 → 2406
      Cadherin_3; Cadherin-like
      cl02522
      Location:2798 → 2894
      Calx-beta; Calx-beta domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      78057323..78544269
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      81398139..81879833
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_020875.1: Suppressed sequence

      Description
      NM_020875.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    2. NM_032863.2: Suppressed sequence

      Description
      NM_032863.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    3. NM_206841.1: Suppressed sequence

      Description
      NM_206841.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86XX4.2 GenPept UniProtKB/Swiss-Prot:Q86XX4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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