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

Gene ID: 23143, updated on 3-Nov-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
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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 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)

Genotypes

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

  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

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