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

    Gene ID: 23143, updated on 9-Dec-2024

    Summary

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    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; AllianceGenome:HGNC:20309
    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
    mouse all
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    Genomic context

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    See LRCH1 in Genome Data Viewer
    Location:
    13q14.13-q14.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (46553170..46753041)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (45774368..45974291)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (47127305..47327176)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903171 Neighboring gene FKBP prolyl isomerase 1A pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5323 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:47127762-47128462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:47192746-47193250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:47193251-47193753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7712 Neighboring gene uncharacterized LOC107984563 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:47370431-47371032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7713 Neighboring gene esterase D

    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. Association between a variation in LRCH1 and knee osteoarthritis: a genome-wide single-nucleotide polymorphism association study using DNA pooling. Spector TD, et al. Arthritis Rheum, 2006 Feb. PMID 16447229
    2. Genetic association analysis of LRCH1 as an osteoarthritis susceptibility locus. Snelling S, et al. Rheumatology (Oxford), 2007 Feb. PMID 16891653
    3. LRCH1 polymorphisms linked to delayed encephalopathy after acute carbon monoxide poisoning identified by GWAS analysis followed by Sequenom MassARRAY® validation. Gu J, et al. BMC Med Genet, 2019 Dec 16. PMID 31842790, Free PMC Article
    4. New gene associations in osteoarthritis: what do they provide, and where are we going? Ikegawa S. Curr Opin Rheumatol, 2007 Sep. PMID 17762607
    5. Lack of association of single nucleotide polymorphism in LRCH1 with knee osteoarthritis susceptibility. Jiang Q, et al. J Hum Genet, 2008. PMID 18049793

    See all (53) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LRCH1 suppresses migration of CD4(+) T cells and refers to disease activity in ulcerative colitis.
      Title: LRCH1 suppresses migration of CD4(+) T cells and refers to disease activity in ulcerative colitis.
    2. LRCH1 deficiency enhances LAT signalosome formation and CD8(+) T cell responses against tumors and pathogens.
      Title: LRCH1 deficiency enhances LAT signalosome formation and CD8(+) T cell responses against tumors and pathogens.
    3. found a significant association between the four LRCH1 polymorphisms and delayed encephalopathy after acute carbon monoxide poisoning (DEACMP). The allelic A of rs9534475 polymorphism in LRCH1 might be a risk factor for DEACMP
      Title: LRCH1 polymorphisms linked to delayed encephalopathy after acute carbon monoxide poisoning identified by GWAS analysis followed by Sequenom MassARRAY® validation.
    4. In the analysis of hip osteoarthritis cases with superior maximum joint space narrowing (JSN) versus cases with non-superior maximum JSN we detected association with a variant in the LRCH1 gene.
      Title: Radiographic endophenotyping in hip osteoarthritis improves the precision of genetic association analysis.
    5. Letter: Did not observe an association between LRCH-1 SNPs and knee osteoarthritis.
      Title: Genetic association analysis of LRCH-1 for knee osteoarthritis.
    6. Meta-analysis and HuGE review of gene-disease association. (HuGE Navigator)
      Title: Field synopsis and synthesis of genetic association studies in osteoarthritis: the CUMAGAS-OSTEO information system.
    7. results suggest that there is no association between LRCH1 and knee osteoarthritis susceptibility
      Title: Lack of association of single nucleotide polymorphism in LRCH1 with knee osteoarthritis susceptibility.
    8. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Association between a variation in LRCH1 and knee osteoarthritis: a genome-wide single-nucleotide polymorphism association study using DNA pooling.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic association analysis of LRCH1 as an osteoarthritis susceptibility locus.
    10. A genetic variant in LRCH1 was consistently associated with knee osteoarthritis in 3 samples from 2 populations.
      Title: Association between a variation in LRCH1 and knee osteoarthritis: a genome-wide single-nucleotide polymorphism association study using DNA pooling.
    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
    Genetic determinants of P wave duration and PR segment.
    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

    Clone Names

    • FLJ41660, KIAA1016

    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 cellular response to chemokine IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cellular response to chemokine IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of T cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of T cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    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)

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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.

    Genomic

    1. NG_021335.2 RefSeqGene

      Range
      5002..196730
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001164211.2 → NP_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
      UniProtKB/TrEMBL
      A8KA33
      Related
      ENSP00000374447.3, ENST00000389797.8
      Conserved Domains (4) summary
      smart00033
      Location:615 → 704
      CH; Calponin homology domain
      sd00033
      Location:76 → 98
      LRR_RI; leucine-rich repeat [structural motif]
      cl26018
      Location:71 → 274
      NEL; C-terminal novel E3 ligase, LRR-interacting
      cl26761
      Location:311 → 513
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

    2. NM_001164213.2 → NP_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
      UniProtKB/TrEMBL
      A8KA33
      Related
      ENSP00000308493.5, ENST00000311191.10
      Conserved Domains (4) summary
      PRK15370
      Location:71 → 274
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:580 → 685
      CH; Calponin homology domain
      COG5271
      Location:311 → 601
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
      sd00033
      Location:76 → 98
      LRR_RI; leucine-rich repeat [structural motif]

    3. NM_015116.3 → NP_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
      UniProtKB/Swiss-Prot
      B7ZLL5, F8W6F0, Q17R43, Q2KHR1, Q5TBU9, Q7Z5F6, Q7Z5F7, Q9Y2L9
      UniProtKB/TrEMBL
      A8KA33
      Related
      ENSP00000374448.3, ENST00000389798.7
      Conserved Domains (4) summary
      PRK15370
      Location:71 → 274
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:580 → 669
      CH; Calponin homology domain
      COG5271
      Location:311 → 601
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
      sd00033
      Location:76 → 98
      LRR_RI; leucine-rich repeat [structural motif]

    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_000013.11 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

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

      UniProtKB/TrEMBL
      A8KA33

    2. XM_047430214.1 → XP_047286170.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      45774368..45974291
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374310.1 → XP_054230285.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A8KA33

    2. XM_054374311.1 → XP_054230286.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y2L9.3 GenPept UniProtKB/Swiss-Prot:Q9Y2L9

    Gene LinkOut

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

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