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    LRCH1 leucine rich repeats and calponin homology domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 23143, updated on 4-Oct-2020

    Summary

    Official Symbol
    LRCH1provided by HGNC
    Official Full Name
    leucine rich repeats and calponin homology domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:20309
    See related
    Ensembl:ENSG00000136141 MIM:610368
    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
    NP81; CHDC1
    Summary
    This gene encodes a protein with a leucine-rich repeat and a calponin homology domain. Polymorphism in this gene may be associated with susceptibililty to knee osteoarthritis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2010]
    Expression
    Ubiquitous expression in endometrium (RPKM 5.5), placenta (RPKM 5.5) and 25 other tissues See more
    Orthologs

    Genomic context

    See LRCH1 in Genome Data Viewer
    Location:
    13q14.13-q14.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    109.20200815 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (46553170..46753041)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (47127296..47327176)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene COX17 pseudogene 1 Neighboring gene FKBP prolyl isomerase 1A pseudogene 3 Neighboring gene uncharacterized LOC107984563 Neighboring gene esterase D

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Genetic determinants of P wave duration and PR segment.
    GeneReviews: Not available

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ41660, KIAA1016

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    cellular response to chemokine IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cellular response to chemokine IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of T cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of T cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytoplasm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    Preferred Names
    leucine-rich repeat and calponin homology domain-containing protein 1
    Names
    leucine-rich repeats and calponin homology (CH) domain containing 1
    neuronal protein 81

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_021335.1 RefSeqGene

      Range
      5001..204881
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001164211.2NP_001157683.2  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL136958, AL138704, AL359880
      Consensus CDS
      CCDS53865.1
      Related
      ENSP00000374447.3, ENST00000389797.8
      Conserved Domains (4) summary
      smart00033
      Location:615704
      CH; Calponin homology domain
      sd00033
      Location:7698
      LRR_RI; leucine-rich repeat [structural motif]
      cl26018
      Location:71274
      NEL; C-terminal novel E3 ligase, LRR-interacting
      cl26761
      Location:311513
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
    2. NM_001164213.2NP_001157685.2  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon and uses an alternate 3' exon, compared to variant 1. These differences result in a distinct 3' UTR, compared to variant 1, and a shorter protein (isoform 3) with a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL136958, AL138704, AL359880
      Consensus CDS
      CCDS53866.1
      Related
      ENSP00000308493.5, ENST00000311191.10
      Conserved Domains (4) summary
      PRK15370
      Location:71274
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:580685
      CH; Calponin homology domain
      COG5271
      Location:311601
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
      sd00033
      Location:7698
      LRR_RI; leucine-rich repeat [structural motif]
    3. NM_015116.3NP_055931.2  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
      Source sequence(s)
      AL136958, AL138704, AL359880
      Consensus CDS
      CCDS31972.1
      Related
      ENSP00000374448.3, ENST00000389798.7
      Conserved Domains (4) summary
      PRK15370
      Location:71274
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:580669
      CH; Calponin homology domain
      COG5271
      Location:311601
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
      sd00033
      Location:7698
      LRR_RI; leucine-rich repeat [structural motif]

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

      Range
      46553170..46753041
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017020483.2XP_016875972.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X1

    2. XM_017020484.1XP_016875973.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X2

    RNA

    1. XR_001749525.2 RNA Sequence

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