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] See more...

Aliases for LRCH1 Gene

Aliases for LRCH1 Gene

  • Leucine Rich Repeats And Calponin Homology Domain Containing 1 2 3 5
  • Leucine-Rich Repeat And Calponin Homology Domain-Containing Protein 1 3 4
  • Leucine-Rich Repeats And Calponin Homology (CH) Domain Containing 1 2 3
  • Neuronal Protein 81 3 4
  • KIAA1016 2 4
  • CHDC1 3 4
  • NP81 3 4
  • Calponin Homology Domain-Containing Protein 1 4
  • Calponin Homology (CH) Domain Containing 1 2
  • LRCH1 5

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 LRCH3.

UniProtKB/Swiss-Prot Summary for LRCH1 Gene

  • Acts as a negative regulator of GTPase CDC42 by sequestering CDC42-guanine exchange factor DOCK8. Probably by preventing CDC42 activation, negatively regulates CD4(+) T-cell migration.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRCH1 Gene

Genomics for LRCH1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LRCH1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH13J046552 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 258 +0.7 733 5 ZNF654 IKZF1 ZNF600 ZNF580 ATF2 POLR2A ZBTB10 YY1 CTCF REST LRCH1 RUBCNL LINC01198 LCP1 lnc-LRRC63-4 ESD
GH13J046664 Enhancer 1.4 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 20.8 +113.9 113891 5.2 ZNF600 ZIC2 FOXA1 FEZF1 FOXA2 KDM6A SAP130 TEAD3 EBF1 ZNF843 LRCH1 LCP1 RUBCNL HSALNG0096893 piR-41245-072 ESD
GH13J046683 Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 20 +133.0 132968 5.9 NCOR1 JUND CEBPA ATF3 NFIC YY1 HES1 BHLHE40 FEZF1 ZEB1 HSALNG0096893 LRCH1 piR-41245-072 ESD
GH13J046678 Promoter/Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 19.7 +126.6 126616 2.5 ZNF600 YY1 SIN3A FEZF1 HOMEZ CTCF FOXA2 RXRA SMC3 EBF1 LRCH1 HSALNG0096893 piR-41245-072 ESD
GH13J046675 Enhancer 1.2 Ensembl ENCODE dbSUPER 18.6 +122.8 122833 2 ZNF600 ZNF580 ATF2 CEBPA ZNF10 ATF3 YY1 FEZF1 ZNF639 ZNF610 LRCH1 HSALNG0096893 piR-41245-072 ESD
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRCH1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRCH1

Top Transcription factor binding sites by QIAGEN in the LRCH1 gene promoter:
  • AhR
  • Arnt
  • Cart-1
  • FOXJ2
  • FOXJ2 (long isoform)
  • IRF-1
  • Lmo2
  • STAT3
  • ZIC2
  • Zic3

Genomic Locations for LRCH1 Gene

Latest Assembly
chr13:46,553,168-46,753,041
(GRCh38/hg38)
Size:
199,874 bases
Orientation:
Plus strand

Previous Assembly
chr13:47,127,305-47,327,176
(GRCh37/hg19 by Entrez Gene)
Size:
199,872 bases
Orientation:
Plus strand

chr13:47,127,303-47,327,175
(GRCh37/hg19 by Ensembl)
Size:
199,873 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:
    • Interacts (via LRR repeats) with unphosphorylated DOCK8 (via DHR-2 domain); the interaction prevents the interaction between DOCK8 and CDC42.
    SequenceCaution:
    • Sequence=BAA76860.1; Type=Erroneous initiation; Note=Extended N-terminus.; 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

Gene Families for LRCH1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for LRCH1 Gene

InterPro:
Blocks:
  • Calponin-like actin-binding

Suggested Antigen Peptide Sequences for LRCH1 Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich repeats and calponin homology (CH) domain containing 1 (B1ALE7_HUMAN)
  • LRCH1 protein (B7ZLL5_HUMAN)
  • Neuronal protein 81 (LRCH1_HUMAN)
  • LRCH1 protein (Q17R43_HUMAN)
  • LRCH1 protein (Q8TAR8_HUMAN)
genes like me logo Genes that share domains with LRCH1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LRCH1 Gene

Function for LRCH1 Gene

Molecular function for LRCH1 Gene

UniProtKB/Swiss-Prot Function:
Acts as a negative regulator of GTPase CDC42 by sequestering CDC42-guanine exchange factor DOCK8. Probably by preventing CDC42 activation, negatively regulates CD4(+) T-cell migration.

Phenotypes From GWAS Catalog for LRCH1 Gene

Gene Ontology (GO) - Molecular Function for LRCH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 24255178
genes like me logo Genes that share ontologies with LRCH1: view
genes like me logo Genes that share phenotypes with LRCH1: view

Animal Models for LRCH1 Gene

MGI Knock Outs for LRCH1:
  • Lrch1 Lrch1<tm1b(EUCOMM)Hmgu>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRCH1

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

Localization for LRCH1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRCH1 Gene

Cytoplasm.

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 3
cytosol 3
cytoskeleton 2
nucleus 2
extracellular 1
mitochondrion 1
endoplasmic reticulum 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
  • Cytosol (2)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LRCH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA,IMP 28028151
genes like me logo Genes that share ontologies with LRCH1: view

Pathways & Interactions for LRCH1 Gene

PathCards logo

SuperPathways for LRCH1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRCH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034260 negative regulation of GTPase activity IEA,IDA 28028151
GO:1990869 cellular response to chemokine IBA,IMP 28028151
GO:2000405 negative regulation of T cell migration IBA,IMP 28028151
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

Drugs & Compounds for LRCH1 Gene

No Compound Related Data Available

Transcripts for LRCH1 Gene

mRNA/cDNA for LRCH1 Gene

3 REFSEQ mRNAs :
19 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRCH1

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

No ASD Table

Relevant External Links for LRCH1 Gene

GeneLoc Exon Structure for
LRCH1

Expression for LRCH1 Gene

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



Protein tissue co-expression partners for LRCH1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRCH1

SOURCE GeneReport for Unigene cluster for LRCH1 Gene:

Hs.507971

Evidence on tissue expression from TISSUES for LRCH1 Gene

  • Nervous system(4.4)
  • Lung(4.2)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with LRCH1: view

Primer products for research

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 29 30
  • 99.43 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LRCH1 29 30
  • 91.14 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LRCH1 29 30
  • 88.26 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lrch1 29
  • 84.64 (n)
Oppossum
(Monodelphis domestica)
Mammalia LRCH1 30
  • 84 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Lrch1 29 16 30
  • 82.43 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LRCH1 30
  • 82 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LRCH1 30
  • 77 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lrch1 29
  • 68.86 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.19625 29
Zebrafish
(Danio rerio)
Actinopterygii si:ch211-260b17.8 29
  • 62.44 (n)
LRCH1 30
  • 59 (a)
OneToOne
Species where no ortholog for LRCH1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for LRCH1: view image
Alliance of Genome Resources:
Additional Orthologs for LRCH1

Paralogs for LRCH1 Gene

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

  • LRCH1_HUMAN
  • C9J5B8_HUMAN
  • C9JWE0_HUMAN
  • Q8TAR8_HUMAN
genes like me logo Genes that share paralogs with LRCH1: view

Variants for LRCH1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRCH1 Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
rs34554559 Benign: not provided 46,694,940(+) A/C
NM_001164211.2(LRCH1):c.1168A>C (p.Ser390Arg)
MISSENSE
rs842380 Benign: not provided 46,685,996(+) A/G
NM_001164211.2(LRCH1):c.777A>G (p.Gln259=)
SYNONYMOUS
rs11617392 -- p.Ala486Ser
rs842381 -- p.Ser234Pro

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LRCH1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for LRCH1 Gene

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

SNP Genotyping and Copy Number Assays for research

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: COP and GCD

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

Additional Disease Information for LRCH1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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 research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4
  2. LRCH1 interferes with DOCK8-Cdc42-induced T cell migration and ameliorates experimental autoimmune encephalomyelitis. (PMID: 28028151) Xu X … Wang H (The Journal of experimental medicine 2017) 3 4
  3. Field synopsis and synthesis of genetic association studies in osteoarthritis: the CUMAGAS-OSTEO information system. (PMID: 20237151) Zintzaras E … Karachalios T (American journal of epidemiology 2010) 3 40
  4. Lack of association of single nucleotide polymorphism in LRCH1 with knee osteoarthritis susceptibility. (PMID: 18049793) Jiang Q … Ikegawa S (Journal of human genetics 2008) 3 40
  5. Genetic association analysis of LRCH1 as an osteoarthritis susceptibility locus. (PMID: 16891653) Snelling S … Loughlin J (Rheumatology (Oxford, England) 2007) 3 40

Products for LRCH1 Gene

Sources for LRCH1 Gene