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    EFEMP1 EGF containing fibulin extracellular matrix protein 1 [ Homo sapiens (human) ]

    Gene ID: 2202, updated on 3-Nov-2024

    Summary

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    Official Symbol
    EFEMP1provided by HGNC
    Official Full Name
    EGF containing fibulin extracellular matrix protein 1provided by HGNC
    Primary source
    HGNC:HGNC:3218
    See related
    Ensembl:ENSG00000115380 MIM:601548; AllianceGenome:HGNC:3218
    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
    DHRD; DRAD; FBNL; MLVT; MTLV; S1-5; FBLN3; GLC1H; ARCL1D; FIBL-3
    Summary
    This gene encodes a member of the fibulin family of extracellular matrix glycoproteins. Like all members of this family, the encoded protein contains tandemly repeated epidermal growth factor-like repeats followed by a C-terminus fibulin-type domain. This gene is upregulated in malignant gliomas and may play a role in the aggressive nature of these tumors. Mutations in this gene are associated with Doyne honeycomb retinal dystrophy. Alternatively spliced transcript variants that encode the same protein have been described.[provided by RefSeq, Nov 2009]
    Expression
    Broad expression in placenta (RPKM 172.1), lung (RPKM 80.6) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EFEMP1 in Genome Data Viewer
    Location:
    2p16.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (55865967..55923782, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (55862877..55920674, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (56093102..56150917, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:55877194-55877806 Neighboring gene polyribonucleotide nucleotidyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15787 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:55935598-55935772 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:55944176-55944368 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:55950709-55951210 Neighboring gene uncharacterized LOC107985811 Neighboring gene uncharacterized LOC112268416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:56063682-56064458 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:56064459-56065235 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:56150477-56150976 Neighboring gene uncharacterized LOC105374690 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:56178767-56179966 Neighboring gene RN7SK pseudogene 208 Neighboring gene MIR217 host gene Neighboring gene microRNA 217

    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 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. Epidermal growth factor-containing fibulin-like extracellular matrix protein 1 expression and regulation in uterine leiomyoma. Marsh EE, et al. Fertil Steril, 2016 Apr. PMID 26702771, Free PMC Article
    2. Influence of differentially expressed genes from suicide post-mortem study on personality traits as endophenotypes on healthy subjects and suicide attempters. Calati R, et al. Eur Arch Psychiatry Clin Neurosci, 2014 Aug. PMID 24241531
    3. EFEMP1 induces γ-secretase/Notch-mediated temozolomide resistance in glioblastoma. Hiddingh L, et al. Oncotarget, 2014 Jan 30. PMID 24495907, Free PMC Article
    4. Novel tumor-suppressor gene epidermal growth factor-containing fibulin-like extracellular matrix protein 1 is epigenetically silenced and associated with invasion and metastasis in human gastric cancer. Zhu XJ, et al. Mol Med Rep, 2014 Jun. PMID 24718752
    5. Epigenetic regulation of EFEMP1 in prostate cancer: biological relevance and clinical potential. Almeida M, et al. J Cell Mol Med, 2014 Nov. PMID 25211630, Free PMC Article

    See all (197) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinicopathological Appearance of Epidermal Growth-Factor-Containing Fibulin-like Extracellular Matrix Protein 1 Deposition in the Lower Gastrointestinal Tract: An Autopsy-Based Study.
      Title: Clinicopathological Appearance of Epidermal Growth-Factor-Containing Fibulin-like Extracellular Matrix Protein 1 Deposition in the Lower Gastrointestinal Tract: An Autopsy-Based Study.
    2. Replication study identified EFEMP1 association with varicose vein predisposition among Indians.
      Title: Replication study identified EFEMP1 association with varicose vein predisposition among Indians.
    3. EFEMP1 haploinsufficiency causes a Marfan-like hereditary connective tissue disorder.
      Title: EFEMP1 haploinsufficiency causes a Marfan-like hereditary connective tissue disorder.
    4. Stop codon variant in EFEMP1 is associated with primary open-angle glaucoma due to impaired regulation of aqueous humor outflow.
      Title: Stop codon variant in EFEMP1 is associated with primary open-angle glaucoma due to impaired regulation of aqueous humor outflow.
    5. A new genetic locus (GLC1H) for adult-onset POAG (primary open-angle glaucoma) maps to the 2p15-p16 region.
      Title: A new locus (GLC1H) for adult-onset primary open-angle glaucoma maps to the 2p15-p16 region.
    6. Mutations in EFEMP1 in Patients with Juvenile Open-Angle Glaucoma.
      Title: Mutations in EFEMP1 in Patients with Juvenile Open-Angle Glaucoma.
    7. Fibulin-3 is necessary to prevent cardiac rupture following myocardial infarction.
      Title: Fibulin-3 is necessary to prevent cardiac rupture following myocardial infarction.
    8. A loss-of-function cysteine mutant in fibulin-3 (EFEMP1) forms aberrant extracellular disulfide-linked homodimers and alters extracellular matrix composition.
      Title: A loss-of-function cysteine mutant in fibulin-3 (EFEMP1) forms aberrant extracellular disulfide-linked homodimers and alters extracellular matrix composition.
    9. Impact of EFEMP1 on the survival outcome of biliary atresia in Thai infants.
      Title: Impact of EFEMP1 on the survival outcome of biliary atresia in Thai infants.
    10. Fibulin-3 sponges Tiam1 to manipulate MMP-7 activity through beta-catenin signaling in oral squamous cell carcinoma.
      Title: Fibulin-3 sponges Tiam1 to manipulate MMP-7 activity through β-catenin signaling in oral squamous cell carcinoma.
    Submit: New GeneRIF Correction See all GeneRIFs (122)

    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
    Cutis laxa, autosomal recessive, type 1d
    MedGen: CN377272 OMIM: 620780 GeneReviews: Not available
    		not available
    Doyne honeycomb retinal dystrophy
    MedGen: C1832174 OMIM: 126600 GeneReviews: Not available
    		Compare labs
    Glaucoma 1, open angle, H
    MedGen: C1969811 OMIM: 611276 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
    EBI GWAS Catalog
    A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis.
    EBI GWAS Catalog
    A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits.
    EBI GWAS Catalog
    Genome-wide association analysis identifies 20 loci that influence adult height.
    EBI GWAS Catalog
    Genome-wide association analysis identifies six new loci associated with forced vital capacity.
    EBI GWAS Catalog
    Genome-wide association study of height and body mass index in Australian twin families.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Identification of 15 loci influencing height in a Korean population.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog
    Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 is identified to have a physical interaction with EGF containing fibulin-like extracellular matrix protein 1 (EFEMP1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ35535, MGC111353

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables epidermal growth factor receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables epidermal growth factor receptor binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables extracellular matrix structural constituent RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    enables growth factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in camera-type eye development IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in embryonic eye morphogenesis IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in epidermal growth factor receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of chondrocyte differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in peptidyl-tyrosine phosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in post-embryonic eye morphogenesis IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in visual perception TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    colocalizes_with collagen-containing extracellular matrix HDA PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in extracellular matrix IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in extracellular region HDA PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular space HDA PubMed 
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    EGF-containing fibulin-like extracellular matrix protein 1
    Names
    EGF containing fibulin like extracellular matrix protein 1
    extracellular protein S1-5
    fibulin-3
    glaucoma 1, open angle, H (adult-onset)

    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_009098.1 RefSeqGene

      Range
      5016..62831
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001039348.3 → NP_001034437.1  EGF-containing fibulin-like extracellular matrix protein 1 precursor

      See identical proteins and their annotated locations for NP_001034437.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longer transcript. Variants 2 and 3 encode the same protein.
      Source sequence(s)
      AC010895, AK290599, AK312639, U03877
      Consensus CDS
      CCDS1857.1
      UniProtKB/Swiss-Prot
      A8K3I4, B4DW75, D6W5D2, Q12805, Q541U7
      UniProtKB/TrEMBL
      A0A0S2Z4F1, A8KAJ3, B2R6M6
      Related
      ENSP00000347596.3, ENST00000355426.8
      Conserved Domains (3) summary
      smart00179
      Location:214 → 244
      EGF_CA; Calcium-binding EGF-like domain
      pfam07645
      Location:173 → 206
      EGF_CA; Calcium-binding EGF domain
      pfam12662
      Location:274 → 297
      cEGF; Complement Clr-like EGF-like

    2. NM_001039349.3 → NP_001034438.1  EGF-containing fibulin-like extracellular matrix protein 1 precursor

      See identical proteins and their annotated locations for NP_001034438.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 2. Variants 2 and 3 encode the same protein.
      Source sequence(s)
      AC010895, BC014410, DA264704, U03877
      Consensus CDS
      CCDS1857.1
      UniProtKB/Swiss-Prot
      A8K3I4, B4DW75, D6W5D2, Q12805, Q541U7
      UniProtKB/TrEMBL
      A0A0S2Z4F1, A8KAJ3, B2R6M6
      Related
      ENSP00000378058.2, ENST00000394555.6
      Conserved Domains (3) summary
      smart00179
      Location:214 → 244
      EGF_CA; Calcium-binding EGF-like domain
      pfam07645
      Location:173 → 206
      EGF_CA; Calcium-binding EGF domain
      pfam12662
      Location:274 → 297
      cEGF; Complement Clr-like EGF-like

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      55865967..55923782 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017003586.3 → XP_016859075.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0S2Z3V1, A8KAJ3, B2R6M6
      Conserved Domains (2) summary
      smart00179
      Location:214 → 253
      EGF_CA; Calcium-binding EGF-like domain
      pfam07645
      Location:173 → 206
      EGF_CA; Calcium-binding EGF domain

    2. XM_005264205.5 → XP_005264262.2  EGF-containing fibulin-like extracellular matrix protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0S2Z3V1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      55862877..55920674 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341033.1 → XP_054197008.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0S2Z3V1

    2. XM_054341032.1 → XP_054197007.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0S2Z3V1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_004105.3: Suppressed sequence

      Description
      NM_004105.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.

    2. NM_018894.1: Suppressed sequence

      Description
      NM_018894.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q12805.2 GenPept UniProtKB/Swiss-Prot:Q12805

    Gene LinkOut

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

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