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    EPDR1 ependymin related 1 [ Homo sapiens (human) ]

    Gene ID: 54749, updated on 13-May-2024

    Summary

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    Official Symbol
    EPDR1provided by HGNC
    Official Full Name
    ependymin related 1provided by HGNC
    Primary source
    HGNC:HGNC:17572
    See related
    Ensembl:ENSG00000086289 MIM:619734; AllianceGenome:HGNC:17572
    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
    EPDR; UCC1; MERP1; MERP-1
    Summary
    The protein encoded by this gene is a type II transmembrane protein that is similar to two families of cell adhesion molecules, the protocadherins and ependymins. This protein may play a role in calcium-dependent cell adhesion. This protein is glycosylated, and the orthologous mouse protein is localized to the lysosome. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 8. [provided by RefSeq, Aug 2011]
    Expression
    Broad expression in brain (RPKM 25.1), endometrium (RPKM 24.9) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EPDR1 in Genome Data Viewer
    Location:
    7p14.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (37920640..37951936)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (38061675..38093041)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (37960242..37991538)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene NME/NM23 family member 8 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18107 Neighboring gene secreted frizzled related protein 4 Neighboring gene Sharpr-MPRA regulatory region 10360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:37987061-37987582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:37987583-37988102 Neighboring gene Sharpr-MPRA regulatory region 4879 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:38026488-38027240 Neighboring gene MPRA-validated peak6491 silencer Neighboring gene uncharacterized LOC105375236 Neighboring gene MPRA-validated peak6492 silencer Neighboring gene MPRA-validated peak6493 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:38110217-38110835 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18108 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:38214547-38215746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18109 Neighboring gene Sharpr-MPRA regulatory region 13548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25865 Neighboring gene STARD3 N-terminal like

    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. EPDR1 is related to stages and metastasize in bladder cancer and can be used as a prognostic biomarker. Yang Y, et al. BMC Urol, 2021 Apr 26. PMID 33902536, Free PMC Article
    2. EPDR1 correlates with immune cell infiltration in hepatocellular carcinoma and can be used as a prognostic biomarker. Chen R, et al. J Cell Mol Med, 2020 Oct. PMID 32935479, Free PMC Article
    3. Evaluation of Primary Angle-Closure Glaucoma Susceptibility Loci for Estimating Angle Closure Disease Severity. Liu C, et al. Ophthalmology, 2021 Mar. PMID 32682838
    4. EPDR1 up-regulation in human colorectal cancer is related to staging and favours cell proliferation and invasiveness. Gimeno-Valiente F, et al. Sci Rep, 2020 Feb 28. PMID 32111877, Free PMC Article
    5. Dupuytren's disease susceptibility gene, EPDR1, is involved in myofibroblast contractility. Staats KA, et al. J Dermatol Sci, 2016 Aug. PMID 27245865

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of bone mineral density associated genes with shared genetic architectures across multiple tissues: Functional insights for EPDR1, PKDCC, and SPTBN1.
      Title: Identification of bone mineral density associated genes with shared genetic architectures across multiple tissues: Functional insights for EPDR1, PKDCC, and SPTBN1.
    2. EPDR1 is related to stages and metastasize in bladder cancer and can be used as a prognostic biomarker.
      Title: EPDR1 is related to stages and metastasize in bladder cancer and can be used as a prognostic biomarker.
    3. Evaluation of Primary Angle-Closure Glaucoma Susceptibility Loci for Estimating Angle Closure Disease Severity.
      Title: Evaluation of Primary Angle-Closure Glaucoma Susceptibility Loci for Estimating Angle Closure Disease Severity.
    4. EPDR1 correlates with immune cell infiltration in hepatocellular carcinoma and can be used as a prognostic biomarker.
      Title: EPDR1 correlates with immune cell infiltration in hepatocellular carcinoma and can be used as a prognostic biomarker.
    5. EPDR1 up-regulation in human colorectal cancer is related to staging and favours cell proliferation and invasiveness.
      Title: EPDR1 up-regulation in human colorectal cancer is related to staging and favours cell proliferation and invasiveness.
    6. Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters, such as LolA.
      Title: Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters.
    7. Study results suggest functional involvement of EPDR1 in the etiology of Dupuytren's Disease.
      Title: Dupuytren's disease susceptibility gene, EPDR1, is involved in myofibroblast contractility.
    8. EPDR1 exhibits a pattern of isoform abundance dependent on KRAS G13D and G12D mutations.
      Title: In silico RNA-seq and experimental analyses reveal the differential expression and splicing of EPDR1 and ZNF518B genes in relation to KRAS mutations in colorectal cancer cells.
    9. Results of this study suggest that EPDR1 gene can be added to a growing list of genes associated with Dupuytren's disease development.
      Title: Common variants of the EPDR1 gene and the risk of Dupuytren’s disease.
    10. Shows that the mouse ortholog is a lysosomal protein.
      Title: Demonstration of lysosomal localization for the mammalian ependymin-related protein using classical approaches combined with a novel density shift method.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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

    EBI GWAS Catalog

    Description
    Wnt signaling and Dupuytren's disease.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ganglioside GM1 binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phospholipid binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell-matrix adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in myofibroblast contraction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular region IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosomal lumen IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    mammalian ependymin-related protein 1
    Names
    ependymin related protein 1
    mammalian ependymin related protein 1
    upregulated in colorectal cancer gene 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.

    mRNA and Protein(s)

    1. NM_001242946.2 → NP_001229875.2  mammalian ependymin-related protein 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001229875.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2, also known as MERP1a) has a distinct and shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      AC018634, AY027862, BC000686, DQ914439
      Consensus CDS
      CCDS59051.1
      UniProtKB/Swiss-Prot
      Q9UM22
      UniProtKB/TrEMBL
      Q96J80
      Related
      ENSP00000409211.1, ENST00000423717.1

    2. NM_001242948.2 → NP_001229877.1  mammalian ependymin-related protein 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate 5' exon and thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (3) has a distinct and shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC018634, AK309180, BC000686, DB167672, DB303790
      Consensus CDS
      CCDS59052.1
      UniProtKB/Swiss-Prot
      Q9UM22
      Related
      ENSP00000413359.1, ENST00000425345.1
      Conserved Domains (1) summary
      pfam00811
      Location:31 → 149
      Ependymin; Ependymin

    3. NM_017549.5 → NP_060019.2  mammalian ependymin-related protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_060019.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC018634, AY027862, BC000686, DA938402
      Consensus CDS
      CCDS5454.2
      UniProtKB/Swiss-Prot
      A8K4C0, C9JYS3, Q06BL0, Q99M77, Q9UM22
      Related
      ENSP00000199448.4, ENST00000199448.9
      Conserved Domains (1) summary
      pfam00811
      Location:89 → 210
      Ependymin; Ependymin

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      37920640..37951936
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      38061675..38093041
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UM22.2 GenPept UniProtKB/Swiss-Prot:Q9UM22

    Gene LinkOut

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

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