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    LHFPL3 LHFPL tetraspan subfamily member 3 [ Homo sapiens (human) ]

    Gene ID: 375612, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LHFPL3provided by HGNC
    Official Full Name
    LHFPL tetraspan subfamily member 3provided by HGNC
    Primary source
    HGNC:HGNC:6589
    See related
    Ensembl:ENSG00000187416 MIM:609719; AllianceGenome:HGNC:6589
    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
    LHFPL4
    Summary
    This gene is a member of the lipoma HMGIC fusion partner (LHFP) gene family, which is a subset of the superfamily of tetraspan transmembrane protein encoding genes. Mutations in one LHFP-like gene result in deafness in humans and mice, and a second LHFP-like gene is fused to a high-mobility group gene in a translocation-associated lipoma. A partial gene fragment named LHFPL4 corresponds to a portion of the first exon of this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in brain (RPKM 18.4) and lung (RPKM 1.0) See more
    Orthologs
    mouse all
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    Genomic context

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    See LHFPL3 in Genome Data Viewer
    Location:
    7q22.2-q22.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (104328603..104908561)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (105642866..106223396)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (103969051..104549008)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375435 Neighboring gene Sharpr-MPRA regulatory region 15155 Neighboring gene reelin Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:103301048-103302247 Neighboring gene Sharpr-MPRA regulatory region 11588 Neighboring gene MPRA-validated peak6667 silencer Neighboring gene Sharpr-MPRA regulatory region 1232 Neighboring gene CRISPRi-validated cis-regulatory element chr7.3907 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:103691916-103692125 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:103765716-103765879 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26445 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:103904410-103905609 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:103916337-103917536 Neighboring gene origin recognition complex subunit 5 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:104001319-104001836 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:104169841-104171040 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:104190573-104191772 Neighboring gene eukaryotic translation initiation factor 4B pseudogene 6 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:104412644-104413408 Neighboring gene LHFPL3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26446 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:104550626-104550782 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:104575494-104575658 Neighboring gene uncharacterized LOC101927902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26448 Neighboring gene Sharpr-MPRA regulatory region 8680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26451 Neighboring gene LHFPL3 antisense RNA 2 Neighboring gene RNA, 7SL, cytoplasmic 8, pseudogene

    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. MiR-218-5p targets LHFPL3 to regulate proliferation, migration, and epithelial-mesenchymal transitions of human glioma cells. Li Z, et al. Biosci Rep, 2019 Mar 29. PMID 30314994, Free PMC Article
    2. LHFP, a novel translocation partner gene of HMGIC in a lipoma, is a member of a new family of LHFP-like genes. Petit MM, et al. Genomics, 1999 May 1. PMID 10329012
    3. GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Rietveld CA, et al. Science, 2013 Jun 21. PMID 23722424, Free PMC Article
    4. A genome-wide association study on obesity and obesity-related traits. Wang K, et al. PLoS One, 2011 Apr 28. PMID 21552555, Free PMC Article
    5. A missense mutation in the previously undescribed gene Tmhs underlies deafness in hurry-scurry (hscy) mice. Longo-Guess CM, et al. Proc Natl Acad Sci U S A, 2005 May 31. PMID 15905332, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Results show that miR-218-5p targeting lipoma HMGIC fusion partner-like 3 protein (LHFPL3) mRNA plays significant roles in preventing the invasiveness of glioma cells.
      Title: MiR-218-5p targets LHFPL3 to regulate proliferation, migration, and epithelial-mesenchymal transitions of human glioma cells.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: High-density SNP association study and copy number variation analysis of the AUTS1 and AUTS5 loci implicate the IMMP2L-DOCK4 gene region in autism susceptibility.
    4. The authors present an overview of the LHFP gene family in mouse and humans
      Title: A missense mutation in the previously undescribed gene Tmhs underlies deafness in hurry-scurry (hscy) mice.
    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
    A genome-wide association study on obesity and obesity-related traits.
    EBI GWAS Catalog
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    EBI GWAS Catalog
    GWAS of 126,559 individuals identifies genetic variants associated with educational attainment.
    EBI GWAS Catalog
    Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
    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)

    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 binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in sensory perception of sound IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    LHFPL tetraspan subfamily member 3 protein
    Names
    LHFP-like protein 3
    lipoma HMGIC fusion partner-like 3 protein
    lipoma HMGIC fusion partner-like 4

    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_001386065.1 → NP_001372994.1  LHFPL tetraspan subfamily member 3 protein isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC002432, AC007384, AC079796, AC091286
      Consensus CDS
      CCDS94167.1
      UniProtKB/TrEMBL
      A1L384, C9JA52
      Related
      ENSP00000385374.3, ENST00000401970.3
      Conserved Domains (1) summary
      pfam10242
      Location:36 → 213
      L_HMGIC_fpl; Lipoma HMGIC fusion partner-like protein

    2. NM_199000.3 → NP_945351.1  LHFPL tetraspan subfamily member 3 protein isoform 1

      See identical proteins and their annotated locations for NP_945351.1

      Status: REVIEWED

      Source sequence(s)
      AC002432, AC007384, AC079796
      Consensus CDS
      CCDS94168.1
      UniProtKB/Swiss-Prot
      A1L383, A4D0Q5, Q86UP9
      Related
      ENSP00000393128.2, ENST00000424859.7
      Conserved Domains (1) summary
      pfam10242
      Location:36 → 213
      L_HMGIC_fpl; Lipoma HMGIC fusion partner-like protein

    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
      104328603..104908561
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      105642866..106223396
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86UP9.3 GenPept UniProtKB/Swiss-Prot:Q86UP9

    Gene LinkOut

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

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