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LHFP (lipoma HMGIC fusion partner)

Identity

HGNC (Hugo) LHFP
Location 13q12
Location_base_pair Starts at 38815029 and ends at 39075356 bp from pter ( according to hg18-Mar_2006)  [Mapping]

DNA/RNA

Description Exon-intron structure not described.
Transcription mRNA: ubiquitously: 2.4 kb; The ATG start codon is immediately preceded by an in-frame stop codon, and matches the most important positions of the Kozak consensus sequence; the 3'-UTR contains a CA-repeat.
Pseudogene No pseudogenes according to pseudogene.org.

Protein

  200 amino acids.
Description Database searches with the predicted LHFP amino acid sequences revealed no significant similarity to any known gene or protein or any known protein motif.
Expression Not known.
Localisation Not known.
Function Not known.
Homology LHFP is a member of a family of proteins, which contains 6 members: LHFP, LHFPL1, LHFPL2, LHFPL3, LHFPL4, LHFPL5.

Mutations

Somatic HMGA2/LHFP fusion gene encoding the three DNA-binding domains of HMGA2 followed by 69 amino acids encoded by frame-shifted LHFP sequences.

Implicated in

Entity Solitary lipomas.
Disease Benign tumors of adipose tissue
Prognosis Can be surgically removed with no recurrence in most cases.
Cytogenetics More than 60% of solitary lipomas have an aberrant karyotype: 2/3 of these carry 12q15 rearrangements, most often translocations, affecting the HMGA2 gene:
  • 1/4 of the latter have chromosomal region 3q27-q28 (containing LPP) as 12q15 translocation partner (creating a HMGA2/LPP fusion gene).
  • In the 3/4 others, multiple chromosomes have been found as translocation partner of 12q15, one of these being chromosomal region 13q12 (containing, amongst others, the LHFP gene).
    • Hybrid/Mutated Gene HMGA2/LHFP hybrid gene containing the first three exons of HMGA2, which are followed by exon(s) of LHFP; under the regulation of the HMGA2 promoter.
    Abnormal Protein No known LHFP fusion protein. (HMGA2/LHFP fusion transcripts encode the three DNA-binding domains of HMGA2 followed by 69 amino acids encoded by frame-shifted LHFP sequences).
      

    External links

    Nomenclature
    HGNC (Hugo)LHFP   6586
    Entrez_Gene (NCBI)LHFP  10186  lipoma HMGIC fusion partner
    Cards
    AtlasLHFPID248ch13q12
    GeneCards (Weizmann)LHFP
    Ensembl (Hinxton)ENSG00000183722 [Gene_View]  LHFP [Vega]
    AceView (NCBI)LHFP
    Genatlas (Paris)LHFP
    euGene (Indiana)10186
    SOURCE (Stanford)NM_005780
    Genomic and cartography
    GoldenPath (UCSC)LHFP  -  13q12   chr13:38815029-39075356 -  13q12   [Description]    (hg18-Mar_2006)
    EnsemblLHFP - 13q12 [CytoView]
    Mapping of homologs : NCBILHFP [Mapview]
    OMIM606710   
    Gene and transcription
    Gene : Genbank (Entrez)AF098807 AK129819 AK223369 AK313036 AL137388
    Reference sequence (RefSeq transcript) :SRSNM_005780
    Reference transcript : EntrezNM_005780
    RefSeq genomic : SRSAC_000056 AC_000145 NC_000013 NT_024524 NW_001838073 NW_925473
    RefSeq genomic : EntrezAC_000056 AC_000145 NC_000013 NT_024524 NW_001838073 NW_925473
    Consensus coding sequences : CCDS NCBILHFP
    Cluster EST : UnigeneHs.507798 [ SRS ] Hs.507798 [ NCBI ]
    Alternative Splicing : Fast-db (Paris)3776
    Protein : pattern, domain, 3D structure
    Protein : UniProt/SwissProtQ9Y693 (SRS) Q9Y693 (Expasy) Q9Y693 (Uniprot)
    With graphics : InterProQ9Y693
    Splice isoforms : VarSplice FASTAQ9Y693(VarSplice FASTA)
    Related proteins : CluSTrQ9Y693
    Domain families : Pfam SRS
    Domain families : Pfam Sanger
    Domain families : Pfam NCBI
    Blocks (Seattle)Q9Y693
    Crystal structure of protein : PDB SRS
    Crystal structure of protein : PDBSum
    Crystal structure of protein : IMB
    Crystal structure of protein : PDB RSDB
    HPRD09464
    Protein Interaction databases
    DIP (DOE-UCLA)Q9Y693
    IntAct (EBI)Q9Y693
    Polymorphism : SNP, mutations, diseases
    Single Nucleotide Polymorphism (SNP) : dbSNP NCBILHFP
    SNP : GeneSNP UtahLHFP
    SNP : HGBaseLHFP
    Genetic variants : HAPMAPLHFP
    Somatic Mutations in Cancer : COSMICLHFP 
    Mutations and Diseases : HGMDLHFP
    Hereditary diseases : OMIM606710   
    Hereditary diseases : GENETests606710   
    Diseases : Genetic AssociationLHFP
    General knowledge
    Homologs : HomoloGeneLHFP
    Homology/Alignments : Family Browser UCSCLHFP
    Phylogenetic Trees/Animal Genes : TreeFamLHFP
    Chemical/Protein Interactions : CTD10186
    Keywords Ontology : AmiGODNA binding  membrane  integral to membrane  
    Keywords Ontology : EGO-EBIDNA binding  membrane  integral to membrane  
    Pathways : BIOCARTA
    Pathways : KEGG
    Other databases
    Probes
    Probes : ImagenesLHFP Related clones (RZPD - Berlin)
    Literature
    PubMed8 Pubmed reference(s) in Entrez
    PubGeneLHFP

    Bibliography

    LHFP, a novel translocation partner gene of HMGIC in a lipoma, is a member of a new family of LHFP-like genes.
    Petit MM, Schoenmakers EF, Huysmans C, Geurts JM, Mandahl N, Van de Ven WJ
    Genomics. 1999 ; 57 (3) : 438-441.
    PMID 10329012
     
    Absence of HMGIC-LHFP fusion in pulmonary chondroid hamartomas with aberrations involving chromosomal regions 12q13 through 15 and 13q12 through q14.
    Rogalla P, Lemke I, Bullerdiek J
    Cancer genetics and cytogenetics. 2002 ; 133 (1) : 90-93.
    PMID 11890997
     
    Clustering of deletions on chromosome 13 in benign and low-malignant lipomatous tumors.
    DahlˆŠn A, Debiec-Rychter M, Pedeutour F, Domanski HA, Hˆglund M, Bauer HC, Rydholm A, Sciot R, Mandahl N, Mertens F
    International journal of cancer. Journal international du cancer. 2003 ; 103 (5) : 616-623.
    PMID 12494468
     
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

    Search in all EBI   NCBI

    Contributor(s)

    Written01-2005Marleen Petit

    Citation

    This paper should be referenced as such :
    Petit MM . LHFP (lipoma HMGIC fusion partner). Atlas Genet Cytogenet Oncol Haematol. January 2005 .
    URL : http://AtlasGeneticsOncology.org/Genes/LHFPID248ch13q12.html

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    indexed on : Sat Jun 27 16:38:02 CEST 2009
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