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

Gene ID: 2202, updated on 13-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (55865967..55923782, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (55862877..55920674, complement)
105.20220307 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
  • 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. Impact of EFEMP1 on the survival outcome of biliary atresia in Thai infants. Laochareonsuk W, et al. Sci Rep, 2022 Sep 16. PMID 36114336, Free PMC Article
  2. A loss-of-function cysteine mutant in fibulin-3 (EFEMP1) forms aberrant extracellular disulfide-linked homodimers and alters extracellular matrix composition. Woodard DR, et al. Hum Mutat, 2022 Dec. PMID 35998264, Free PMC Article
  3. Significance of fibulin-3 expression in bladder cancer: a tissue microarray-based immunohistochemical study. Al Khader A, et al. World J Surg Oncol, 2022 Apr 26. PMID 35473807, Free PMC Article
  4. EFEMP1 rare variants cause familial juvenile-onset open-angle glaucoma. Collantes ERA, et al. Hum Mutat, 2022 Feb. PMID 34923728, Free PMC Article
  5. Serum Proteomics and Plasma Fibulin-3 in Differentiation of Mesothelioma From Asbestos-Exposed Controls and Patients With Other Pleural Diseases. Tsim S, et al. J Thorac Oncol, 2021 Oct. PMID 34116230, Free PMC Article

See all (184) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. Mutations in EFEMP1 in Patients with Juvenile Open-Angle Glaucoma.
    Title: Mutations in EFEMP1 in Patients with Juvenile Open-Angle Glaucoma.
  4. Fibulin-3 is necessary to prevent cardiac rupture following myocardial infarction.
    Title: Fibulin-3 is necessary to prevent cardiac rupture following myocardial infarction.
  5. 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.
  6. 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.
  7. 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.
  8. Significance of fibulin-3 expression in bladder cancer: a tissue microarray-based immunohistochemical study.
    Title: Significance of fibulin-3 expression in bladder cancer: a tissue microarray-based immunohistochemical study.
  9. Upregulated Fibulin-1 Increased Endometrial Stromal Cell Viability and Migration by Repressing EFEMP1-Dependent Ferroptosis in Endometriosis.
    Title: Upregulated Fibulin-1 Increased Endometrial Stromal Cell Viability and Migration by Repressing EFEMP1-Dependent Ferroptosis in Endometriosis.
  10. EFEMP1 rare variants cause familial juvenile-onset open-angle glaucoma.
    Title: EFEMP1 rare variants cause familial juvenile-onset open-angle glaucoma.
Submit: New GeneRIF Correction See all GeneRIFs (119)

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 ID
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 TAS
Traceable Author Statement
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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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_2023_10

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

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