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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
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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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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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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

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