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    ELFN1 extracellular leucine rich repeat and fibronectin type III domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 392617, updated on 27-Nov-2024

    Summary

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    Official Symbol
    ELFN1provided by HGNC
    Official Full Name
    extracellular leucine rich repeat and fibronectin type III domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:33154
    See related
    Ensembl:ENSG00000225968 MIM:614964; AllianceGenome:HGNC:33154
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PPP1R28
    Summary
    Predicted to enable protein phosphatase inhibitor activity. Predicted to be involved in synapse organization. Predicted to act upstream of or within synapse assembly; synaptic signaling; and visual perception. Predicted to be located in dendrite and excitatory synapse. Predicted to be active in several cellular components, including axon terminus; glutamatergic synapse; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in liver (RPKM 1.3), kidney (RPKM 0.9) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ELFN1 in Genome Data Viewer
    Location:
    7p22.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (1666064..1747946)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (1778588..1860511)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (1705700..1787582)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375303 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1688785-1689292 Neighboring gene transcription factor A, mitochondrial pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1708637-1709344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1709345-1710051 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1710052-1710758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1710759-1711465 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1744455-1745164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1745165-1745874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1748146-1748646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1748647-1749147 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1752367-1753267 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1753268-1754167 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1756087-1756786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1756787-1757486 Neighboring gene uncharacterized LOC124901819 Neighboring gene uncharacterized LOC105375124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1764307-1764893 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1772549-1773050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25499 Neighboring gene lncRNA radiation induced regulator of PLK1 and RAD51 Neighboring gene ELFN1 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 13438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1847611-1848112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1848113-1848612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1852667-1853242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1878277-1879182 Neighboring gene uncharacterized LOC100127955 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1887449-1888158 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1896343-1897150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1897151-1897958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1897959-1898765 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1900385-1901202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1901203-1902019 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1902954-1903628 Neighboring gene mitotic arrest deficient 1 like 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98143 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1913269-1914241 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1923010-1923799 Neighboring gene microRNA 4655 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:1930511-1931011 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:1930010-1930510 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:1940274-1941134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1951273-1951773 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1951951-1952584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1952585-1953218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1970348-1971296 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_98173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1979601-1980186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1985471-1986286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1986287-1987101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1994453-1995177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1997460-1998140 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:2000936-2002135 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:2019399-2020598 Neighboring gene uncharacterized LOC124901573

    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. ELFN1 is a new extracellular matrix (ECM)-associated protein. Ayhan S, et al. Life Sci, 2024 Sep 1. PMID 38986898
    2. Biallelic mutations in ELFN1 gene associated with developmental and epileptic encephalopathy and joint laxity. Dursun A, et al. Eur J Med Genet, 2021 Nov. PMID 34509675
    3. Synaptic adhesion protein ELFN1 is a selective allosteric modulator of group III metabotropic glutamate receptors in trans. Dunn HA, et al. Proc Natl Acad Sci U S A, 2018 May 8. PMID 29686062, Free PMC Article
    4. The extracellular leucine-rich repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns. Dolan J, et al. BMC Genomics, 2007 Sep 14. PMID 17868438, Free PMC Article
    5. Elfn1 recruits presynaptic mGluR7 in trans and its loss results in seizures. Tomioka NH, et al. Nat Commun, 2014 Jul 22. PMID 25047565

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ELFN1 is a new extracellular matrix (ECM)-associated protein.
      Title: ELFN1 is a new extracellular matrix (ECM)-associated protein.
    2. Biallelic mutations in ELFN1 gene associated with developmental and epileptic encephalopathy and joint laxity.
      Title: Biallelic mutations in ELFN1 gene associated with developmental and epileptic encephalopathy and joint laxity.
    3. the binding specificity of ELFN1 and found it to be recruited selectively to all group III mGluRs (mGluR4, mGluR6, mGluR7, and mGluR8), but not other mGluR species.
      Title: Synaptic adhesion protein ELFN1 is a selective allosteric modulator of group III metabotropic glutamate receptors in trans.
    4. Damaging missense mutations of ELFN1, that are clustered in the carboxy-terminal region required for mGluR7 recruitment, are found in patients with epilepsy and attention deficit hyperactivity disorder.
      Title: Elfn1 recruits presynaptic mGluR7 in trans and its loss results in seizures.
    Submit: New GeneRIF Correction

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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 protein phosphatase inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chemical synaptic transmission IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in establishment of protein localization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synapse assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synapse organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in synaptic membrane adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in axon terminus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in excitatory synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein ELFN1
    Names
    extracellular leucine-rich repeat and fibronectin type III containing 1
    extracellular leucine-rich repeat and fibronectin type-III domain-containing protein 1
    protein phosphatase 1 regulatory subunit 28

    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_001128636.4 → NP_001122108.1  protein ELFN1 precursor

      See identical proteins and their annotated locations for NP_001122108.1

      Status: VALIDATED

      Source sequence(s)
      AC074389
      Consensus CDS
      CCDS59046.1
      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0
      Related
      ENSP00000456548.1, ENST00000424383.5
      Conserved Domains (3) summary
      TIGR00864
      Location:162 → 256
      PCC; polycystin cation channel protein
      sd00031
      Location:65 → 85
      LRR_1; leucine-rich repeat [structural motif]
      pfam13855
      Location:85 → 144
      LRR_8; Leucine rich repeat

    2. NM_001394187.1 → NP_001381116.1  protein ELFN1 precursor

      Status: VALIDATED

      Source sequence(s)
      AC074389
      Consensus CDS
      CCDS59046.1
      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0
      Related
      ENSP00000510296.1, ENST00000691883.1
      Conserved Domains (3) summary
      TIGR00864
      Location:162 → 256
      PCC; polycystin cation channel protein
      sd00031
      Location:65 → 85
      LRR_1; leucine-rich repeat [structural motif]
      pfam13855
      Location:85 → 144
      LRR_8; Leucine rich repeat

    3. NM_001394188.1 → NP_001381117.1  protein ELFN1 precursor

      Status: VALIDATED

      Source sequence(s)
      AC074389
      Consensus CDS
      CCDS59046.1
      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0
      Conserved Domains (3) summary
      TIGR00864
      Location:162 → 256
      PCC; polycystin cation channel protein
      sd00031
      Location:65 → 85
      LRR_1; leucine-rich repeat [structural motif]
      pfam13855
      Location:85 → 144
      LRR_8; Leucine rich repeat

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      1666064..1747946
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006715725.4 → XP_006715788.1  protein ELFN1 isoform X1

      See identical proteins and their annotated locations for XP_006715788.1

      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0
      Related
      ENSP00000457193.1, ENST00000561626.4
      Conserved Domains (3) summary
      TIGR00864
      Location:162 → 256
      PCC; polycystin cation channel protein
      sd00031
      Location:65 → 85
      LRR_1; leucine-rich repeat [structural motif]
      pfam13855
      Location:85 → 144
      LRR_8; Leucine rich repeat

    2. XM_047420363.1 → XP_047276319.1  protein ELFN1 isoform X1

      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0

    3. XM_047420362.1 → XP_047276318.1  protein ELFN1 isoform X1

      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0

    4. XM_011515398.3 → XP_011513700.1  protein ELFN1 isoform X1

      See identical proteins and their annotated locations for XP_011513700.1

      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0
      Conserved Domains (3) summary
      TIGR00864
      Location:162 → 256
      PCC; polycystin cation channel protein
      sd00031
      Location:65 → 85
      LRR_1; leucine-rich repeat [structural motif]
      pfam13855
      Location:85 → 144
      LRR_8; Leucine rich repeat

    5. XM_006715727.4 → XP_006715790.1  protein ELFN1 isoform X1

      See identical proteins and their annotated locations for XP_006715790.1

      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0
      Conserved Domains (3) summary
      TIGR00864
      Location:162 → 256
      PCC; polycystin cation channel protein
      sd00031
      Location:65 → 85
      LRR_1; leucine-rich repeat [structural motif]
      pfam13855
      Location:85 → 144
      LRR_8; Leucine rich repeat

    6. XM_011515401.3 → XP_011513703.1  protein ELFN1 isoform X1

      See identical proteins and their annotated locations for XP_011513703.1

      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0
      Conserved Domains (3) summary
      TIGR00864
      Location:162 → 256
      PCC; polycystin cation channel protein
      sd00031
      Location:65 → 85
      LRR_1; leucine-rich repeat [structural motif]
      pfam13855
      Location:85 → 144
      LRR_8; Leucine rich repeat

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      1778588..1860511
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358197.1 → XP_054214172.1  protein ELFN1 isoform X1

      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0

    2. XM_054358195.1 → XP_054214170.1  protein ELFN1 isoform X1

      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0

    3. XM_054358196.1 → XP_054214171.1  protein ELFN1 isoform X1

      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0

    4. XM_054358198.1 → XP_054214173.1  protein ELFN1 isoform X1

      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0

    5. XM_054358199.1 → XP_054214174.1  protein ELFN1 isoform X1

      UniProtKB/Swiss-Prot
      H3BS57, P0C7U0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0C7U0.2 GenPept UniProtKB/Swiss-Prot:P0C7U0

    Gene LinkOut

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

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