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

Summary

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

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Replication study identified EFEMP1 association with varicose vein predisposition among Indians.
Title: Replication study identified EFEMP1 association with varicose vein predisposition among Indians.
EFEMP1 haploinsufficiency causes a Marfan-like hereditary connective tissue disorder.
Title: EFEMP1 haploinsufficiency causes a Marfan-like hereditary connective tissue disorder.
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.
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.
Mutations in EFEMP1 in Patients with Juvenile Open-Angle Glaucoma.
Title: Mutations in EFEMP1 in Patients with Juvenile Open-Angle Glaucoma.
Fibulin-3 is necessary to prevent cardiac rupture following myocardial infarction.
Title: Fibulin-3 is necessary to prevent cardiac rupture following myocardial infarction.
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.
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.
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	not available
Glaucoma 1, open angle, H MedGen: C1969811 OMIM: 611276 GeneReviews: Not available	not available

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

RH98599 (e-PCR)
- UniSTS:86322

RH93383 (e-PCR)
- UniSTS:90467

D2S2864 (e-PCR)
- UniSTS:9583

D2S2626 (e-PCR)
- UniSTS:36798

RH70532 (e-PCR)
- UniSTS:967

SHGC-106202 (e-PCR)
- UniSTS:169698

SHGC-12903 (e-PCR)
- UniSTS:78332

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 more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular matrix	IMP Inferred from Mutant Phenotype more info	PubMed
located_in extracellular region	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	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

NG_009098.1 RefSeqGene

Range

5016..62831

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

55865967..55923782 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A0S2Z3V1

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

55862877..55920674 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A0S2Z3V1
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

NM_004105.3: Suppressed sequence

Description

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