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ELFN2 extracellular leucine rich repeat and fibronectin type III domain containing 2 [ Homo sapiens (human) ]

Gene ID: 114794, updated on 11-Apr-2024

Summary

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Official Symbol
ELFN2provided by HGNC
Official Full Name
extracellular leucine rich repeat and fibronectin type III domain containing 2provided by HGNC
Primary source
HGNC:HGNC:29396
See related
Ensembl:ENSG00000166897 MIM:620223; AllianceGenome:HGNC:29396
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
LRRC62; PPP1R29
Summary
Predicted to enable protein phosphatase inhibitor activity. Predicted to be involved in negative regulation of catalytic activity. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 10.0) and testis (RPKM 1.9) See more
Orthologs
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Genomic context

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See ELFN2 in Genome Data Viewer
Location:
22q13.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (37340644..37427479, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (37801164..37887955, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (37736685..37823514, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37656641-37657180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13684 Neighboring gene Sharpr-MPRA regulatory region 14238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18968 Neighboring gene cytohesin 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37705193-37705774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18970 Neighboring gene uncharacterized LOC105373024 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:37707125-37708324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37713975-37714832 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:37723358-37724557 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37725005-37725650 Neighboring gene Sharpr-MPRA regulatory region 3535 Neighboring gene uncharacterized LOC100506271 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37751415-37751915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37750914-37751414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37764078-37765044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37774300-37774868 Neighboring gene uncharacterized LOC124905114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37782078-37782616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37798615-37799363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37806589-37807090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37812286-37812830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37815805-37816474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37816475-37817143 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37863012-37863625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37865281-37865782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37880249-37880758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37882293-37882802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37882803-37883314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37883315-37883824 Neighboring gene MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37898069-37898668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37898669-37899266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37904132-37904960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37904961-37905787 Neighboring gene caspase recruitment domain family member 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37907945-37908458

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. Identification of Key Prognostic-Related miRNA-mRNA Pairs in the Progression of Endometrial Carcinoma. Dong Y, et al. Gynecol Obstet Invest, 2022. PMID 35081534
  2. ELFN2 is a postsynaptic cell adhesion molecule with essential roles in controlling group III mGluRs in the brain and neuropsychiatric behavior. Dunn HA, et al. Mol Psychiatry, 2019 Dec. PMID 31485013, Free PMC Article
  3. 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
  4. Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases. Cobb J, et al. Pharmacogenomics J, 2014 Aug. PMID 24709693, Free PMC Article
  5. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. Nagase T, et al. DNA Res, 2001 Aug 31. PMID 11572484

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of Key Prognostic-Related miRNA-mRNA Pairs in the Progression of Endometrial Carcinoma.
    Title: Identification of Key Prognostic-Related miRNA-mRNA Pairs in the Progression of Endometrial Carcinoma.
  2. Authors conclude that extracellular transsynaptic scaffolding by ELFN2 in the brain is a cardinal organizational feature of group III mGluRs essential for their signaling properties and brain function.
    Title: ELFN2 is a postsynaptic cell adhesion molecule with essential roles in controlling group III mGluRs in the brain and neuropsychiatric behavior.
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

EBI GWAS Catalog

Description
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
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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Replication interactions

Interaction Pubs
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of ELFN2 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

  • FLJ30913, KIAA1904

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein phosphatase inhibitor activity IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space HDA PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein phosphatase 1 regulatory subunit 29
Names
dJ63G5.3 (putative Leucine rich protein)
leucine-rich repeat and fibronectin type-III domain-containing protein 6
leucine-rich repeat-containing protein 62

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_052906.5 → NP_443138.2  protein phosphatase 1 regulatory subunit 29 precursor

    See identical proteins and their annotated locations for NP_443138.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer trancript and encodes the protein.
    Source sequence(s)
    AB067491, BC032082, DA398675, FP325335, Z94160
    Consensus CDS
    CCDS33642.1
    UniProtKB/Swiss-Prot
    Q5R3F8, Q96PY3
    Related
    ENSP00000385277.1, ENST00000402918.7
    Conserved Domains (4) summary
    TIGR00864
    Location:157 → 227
    PCC; polycystin cation channel protein
    sd00031
    Location:60 → 80
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:200 → 226
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:80 → 139
    LRR_8; Leucine rich repeat

RNA

  1. NR_110512.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two exons and contains two alternate 3' terminal exons, compared to variant 1. This variant is represented as non-coding because it lacks the entire coding region found in variant 1.
    Source sequence(s)
    DA365834, DA398675, FP325335, Z94160

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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    37340644..37427479 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    37801164..37887955 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5R3F8.1 GenPept UniProtKB/Swiss-Prot:Q5R3F8

Gene LinkOut

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

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