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

Gene ID: 375612, updated on 5-Mar-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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Location:
7q22.2-q22.3
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (104328603..104908561)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (105642866..106223396)
105.20220307 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)

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 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_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
    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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