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Aliases for LRCH1 Gene

Aliases for LRCH1 Gene

  • Leucine Rich Repeats And Calponin Homology Domain Containing 1 2 3 5
  • Leucine-Rich Repeats And Calponin Homology (CH) Domain Containing 1 2 3
  • Neuronal Protein 81 3 4
  • CHDC1 3 4
  • NP81 3 4
  • Leucine-Rich Repeat And Calponin Homology Domain-Containing Protein 1 3
  • Calponin Homology Domain-Containing Protein 1 4
  • Calponin Homology (CH) Domain Containing 1 2
  • KIAA1016 4

External Ids for LRCH1 Gene

Previous HGNC Symbols for LRCH1 Gene

  • CHDC1

Previous GeneCards Identifiers for LRCH1 Gene

  • GC13P044925
  • GC13P046025
  • GC13P047127
  • GC13P027920

Summaries for LRCH1 Gene

Entrez Gene Summary for LRCH1 Gene

  • 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]

GeneCards Summary for LRCH1 Gene

LRCH1 (Leucine Rich Repeats And Calponin Homology Domain Containing 1) is a Protein Coding gene. Diseases associated with LRCH1 include Osteoarthritis. An important paralog of this gene is LRCH2.

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRCH1 Gene

Genomics for LRCH1 Gene

Regulatory Elements for LRCH1 Gene

Enhancers for LRCH1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH13G046664 1.7 FANTOM5 Ensembl ENCODE dbSUPER 20.8 +113.9 113890 5.3 HDGF HNRNPUL1 TBP PKNOX1 FOXA2 ARID4B FEZF1 NFXL1 ZBTB40 GATA2 LRCH1 LCP1 RUBCNL GC13P046617 ENSG00000278462
GH13G046604 1.5 Ensembl ENCODE dbSUPER 18.7 +54.1 54123 6.2 PKNOX1 FOXA2 MLX WRNIP1 FEZF1 DMAP1 ZNF48 SLC30A9 ZNF766 ELK1 LRCH1 RNU2-6P RUBCNL GC13P046617 GC13P046577
GH13G046687 1.4 Ensembl ENCODE dbSUPER 19.9 +135.2 135174 1.5 FOXA2 MLX ARID4B FEZF1 DMAP1 YY1 TCF12 FOS TSHZ1 SMARCA4 LRCH1 ENSG00000278462 GC13P046617
GH13G046683 1.3 Ensembl ENCODE dbSUPER 20 +132.4 132363 3.6 THRB RAD21 RARA IKZF2 CREM ZNF680 CBFB JUNB CEBPB REST LRCH1 ENSG00000278462 GC13P046617
GH13G046678 1.3 Ensembl ENCODE dbSUPER 19.7 +126.6 126646 2.5 HDGF TBL1XR1 WRNIP1 SIN3A FEZF1 ZNF2 RAD21 YY1 GLIS2 ZEB2 LRCH1 ENSG00000278462 GC13P046617
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LRCH1 on UCSC Golden Path with GeneCards custom track

Promoters for LRCH1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000062417 862 2801 ARID4B SIN3A GLI4 ZNF48 YY1 ZNF121 GLIS2 ZNF263 SP3 REST

Genomic Location for LRCH1 Gene

Chromosome:
13
Start:
46,553,138 bp from pter
End:
46,753,041 bp from pter
Size:
199,904 bases
Orientation:
Plus strand

Genomic View for LRCH1 Gene

Genes around LRCH1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRCH1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRCH1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRCH1 Gene

Proteins for LRCH1 Gene

  • Protein details for LRCH1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2L9-LRCH1_HUMAN
    Recommended name:
    Leucine-rich repeat and calponin homology domain-containing protein 1
    Protein Accession:
    Q9Y2L9
    Secondary Accessions:
    • B7ZLL5
    • F8W6F0
    • Q17R43
    • Q2KHR1
    • Q5TBU9
    • Q7Z5F6
    • Q7Z5F7

    Protein attributes for LRCH1 Gene

    Size:
    728 amino acids
    Molecular mass:
    80875 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA76860.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=CAH70793.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAH73643.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI12229.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for LRCH1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRCH1 Gene

Post-translational modifications for LRCH1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LRCH1 Gene

Domains & Families for LRCH1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LRCH1: view

No data available for Gene Families and UniProtKB/Swiss-Prot for LRCH1 Gene

Function for LRCH1 Gene

Gene Ontology (GO) - Molecular Function for LRCH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with LRCH1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRCH1 Gene

Localization for LRCH1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRCH1 gene
Compartment Confidence
plasma membrane 5
cytosol 3
cytoskeleton 2
nucleus 2
mitochondrion 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for LRCH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IBA --
genes like me logo Genes that share ontologies with LRCH1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for LRCH1 Gene

Pathways & Interactions for LRCH1 Gene

SuperPathways for LRCH1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRCH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IBA --
genes like me logo Genes that share ontologies with LRCH1: view

No data available for Pathways by source and SIGNOR curated interactions for LRCH1 Gene

Transcripts for LRCH1 Gene

Unigene Clusters for LRCH1 Gene

Leucine-rich repeats and calponin homology (CH) domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRCH1 Gene

No ASD Table

Relevant External Links for LRCH1 Gene

GeneLoc Exon Structure for
LRCH1
ECgene alternative splicing isoforms for
LRCH1

Expression for LRCH1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRCH1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LRCH1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (12.6), Retina (6.1), and CD8 Tcells (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LRCH1 Gene



Protein tissue co-expression partners for LRCH1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LRCH1 Gene:

LRCH1

SOURCE GeneReport for Unigene cluster for LRCH1 Gene:

Hs.507971

Evidence on tissue expression from TISSUES for LRCH1 Gene

  • Nervous system(4.3)
  • Lung(4.2)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with LRCH1: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRCH1 Gene

Orthologs for LRCH1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRCH1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRCH1 34 35
  • 99.43 (n)
dog
(Canis familiaris)
Mammalia LRCH1 35 34
  • 91.14 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LRCH1 34 35
  • 88.26 (n)
rat
(Rattus norvegicus)
Mammalia Lrch1 34
  • 84.64 (n)
oppossum
(Monodelphis domestica)
Mammalia LRCH1 35
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lrch1 16 35 34
  • 82.43 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LRCH1 35
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves LRCH1 35
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrch1 34
  • 68.86 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.19625 34
zebrafish
(Danio rerio)
Actinopterygii si:ch211-260b17.8 34
  • 62.44 (n)
LRCH1 35
  • 59 (a)
OneToOne
Species where no ortholog for LRCH1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LRCH1 Gene

ENSEMBL:
Gene Tree for LRCH1 (if available)
TreeFam:
Gene Tree for LRCH1 (if available)

Paralogs for LRCH1 Gene

(7) SIMAP similar genes for LRCH1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with LRCH1: view

Variants for LRCH1 Gene

Sequence variations from dbSNP and Humsavar for LRCH1 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
rs1000021568 -- 46,552,795(+) TCCTG(A/C)CCCAA upstream-variant-2KB
rs1000031111 -- 46,587,448(+) TGATA(A/C)TGCTA intron-variant
rs1000047792 -- 46,594,122(+) GAGTG(A/C/G)CATTG intron-variant
rs1000078406 -- 46,574,351(+) AAATT(A/T)AAAAA intron-variant
rs1000088849 -- 46,722,915(+) AAGAT(A/G)AGTGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LRCH1 Gene

Variant ID Type Subtype PubMed ID
esv1496328 CNV insertion 17803354
esv2747365 CNV deletion 23290073
esv3302644 CNV tandem duplication 20981092
esv3369304 CNV insertion 20981092
esv3440295 CNV duplication 20981092
esv3447922 CNV duplication 20981092
esv3631993 CNV loss 21293372
esv988509 CNV insertion 20482838
nsv1026 CNV insertion 18451855
nsv1150818 CNV insertion 26484159
nsv455876 CNV gain 19166990
nsv561581 CNV gain 21841781

Variation tolerance for LRCH1 Gene

Residual Variation Intolerance Score: 44.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.90; 59.26% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LRCH1 Gene

Human Gene Mutation Database (HGMD)
LRCH1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRCH1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRCH1 Gene

Disorders for LRCH1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LRCH1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
osteoarthritis
  • arthropathy
- elite association - COSMIC cancer census association via MalaCards
Search LRCH1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LRCH1

Genetic Association Database (GAD)
LRCH1
Human Genome Epidemiology (HuGE) Navigator
LRCH1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LRCH1
genes like me logo Genes that share disorders with LRCH1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRCH1 Gene

Publications for LRCH1 Gene

  1. Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10231032) Nagase T. … Ohara O. (DNA Res. 1999) 2 3 4 64
  2. Field synopsis and synthesis of genetic association studies in osteoarthritis: the CUMAGAS-OSTEO information system. (PMID: 20237151) Zintzaras E. … Karachalios T. (Am. J. Epidemiol. 2010) 3 46 64
  3. Lack of association of single nucleotide polymorphism in LRCH1 with knee osteoarthritis susceptibility. (PMID: 18049793) Jiang Q. … Ikegawa S. (J. Hum. Genet. 2008) 3 46 64
  4. Genetic association analysis of LRCH1 as an osteoarthritis susceptibility locus. (PMID: 16891653) Snelling S. … Loughlin J. (Rheumatology (Oxford) 2007) 3 46 64
  5. Association between a variation in LRCH1 and knee osteoarthritis: a genome-wide single-nucleotide polymorphism association study using DNA pooling. (PMID: 16447229) Spector T.D. … Braun A. (Arthritis Rheum. 2006) 3 46 64

Products for LRCH1 Gene

Sources for LRCH1 Gene

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