This gene encodes a member of the leucine-rich repeat and calponin homology domain-containing protein family. These family members contain multiple N-terminal leucine-rich repeats, in addition to a C-terminal calponin homology domain, a type of domain that mediates interactions with actin filaments. These proteins are conserved across animal species, and studies of a similar Dr... See more...

Aliases for LRCH2 Gene

Aliases for LRCH2 Gene

  • Leucine Rich Repeats And Calponin Homology Domain Containing 2 2 3 5
  • Leucine-Rich Repeat And Calponin Homology Domain-Containing Protein 2 3 4
  • Leucine-Rich Repeats And Calponin Homology (CH) Domain Containing 2 2 3
  • KIAA1495 2 4
  • DA204F4.4 3
  • LRCH2 5

External Ids for LRCH2 Gene

Previous GeneCards Identifiers for LRCH2 Gene

  • GC0XM113110
  • GC0XM114168
  • GC0XM114251
  • GC0XM114345
  • GC0XM103930

Summaries for LRCH2 Gene

Entrez Gene Summary for LRCH2 Gene

  • This gene encodes a member of the leucine-rich repeat and calponin homology domain-containing protein family. These family members contain multiple N-terminal leucine-rich repeats, in addition to a C-terminal calponin homology domain, a type of domain that mediates interactions with actin filaments. These proteins are conserved across animal species, and studies of a similar Drosophila protein indicate a function as a cytoskeletal scaffolding protein. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2011]

GeneCards Summary for LRCH2 Gene

LRCH2 (Leucine Rich Repeats And Calponin Homology Domain Containing 2) is a Protein Coding gene. Diseases associated with LRCH2 include Hermansky-Pudlak Syndrome 3 and Separation Anxiety Disorder. An important paralog of this gene is LRCH1.

UniProtKB/Swiss-Prot Summary for LRCH2 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRCH2 Gene

Genomics for LRCH2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LRCH2 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
GH0XJ115966 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 250 -734.4 -734405 4.2 POLR2A YY1 CEBPB ZNF341 ZNF217 SIN3A SP2 RXRA CTCF TBP DANT2 HSALNG0139667 KM192214 LRCH2 AGTR2 PLS3
GH0XJ115233 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +1.0 996 3.4 ZNF600 ZNF10 SIN3A SP2 YY1 PRDM6 ZNF664 ATF2 ZNF366 POLR2A LRCH2 API5P1 IL13RA2 HSALNG0139628 RBMXL3
GH0XJ115559 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 10 -328.0 -327989 5.8 ZNF600 CEBPA ZNF223 ATF3 POLR2A NFIC ZIC2 ZBTB10 YY1 FEZF1 PLS3 HSALNG0139639-002 PLS3-AS1 LRCH2 AGTR2
GH0XJ115344 Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas 11.4 -111.2 -111213 2.3 ZNF600 SSRP1 JUND ZMYM3 CEBPA ATF3 NFIC CHD4 YY1 CEBPB HSALNG0139631-001 HSALNG0139631-002 LOC107985681 LRCH2 piR-54592-315 LUZP4 PLS3
GH0XJ115958 Enhancer 0.9 Ensembl ENCODE 12.6 -725.9 -725905 3.6 ZNF654 CHD2 ZNF341 CTBP1 RAD21 CTCF MAZ ZNF384 HCFC1 TOE1 piR-36564-028 LRCH2 DANT2 KM192214 piR-56133-249 AGTR2 PLS3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRCH2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRCH2

Top Transcription factor binding sites by QIAGEN in the LRCH2 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CP1A
  • Egr-3
  • GR
  • GR-alpha
  • NF-Y
  • NF-YA
  • NF-YB

Genomic Locations for LRCH2 Gene

Latest Assembly
chrX:115,110,611-115,234,096
(GRCh38/hg38)
Size:
123,486 bases
Orientation:
Minus strand

Previous Assembly
chrX:114,345,179-114,468,659
(GRCh37/hg19 by Entrez Gene)
Size:
123,481 bases
Orientation:
Minus strand

chrX:114,345,185-114,468,635
(GRCh37/hg19 by Ensembl)
Size:
123,451 bases
Orientation:
Minus strand

Genomic View for LRCH2 Gene

Genes around LRCH2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRCH2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRCH2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRCH2 Gene

Proteins for LRCH2 Gene

  • Protein details for LRCH2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VUJ6-LRCH2_HUMAN
    Recommended name:
    Leucine-rich repeat and calponin homology domain-containing protein 2
    Protein Accession:
    Q5VUJ6
    Secondary Accessions:
    • F5H2T1
    • Q08AD5
    • Q9HA88
    • Q9P233

    Protein attributes for LRCH2 Gene

    Size:
    765 amino acids
    Molecular mass:
    84588 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA96019.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for LRCH2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRCH2 Gene

Post-translational modifications for LRCH2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LRCH2 Gene

No data available for DME Specific Peptides for LRCH2 Gene

Domains & Families for LRCH2 Gene

Gene Families for LRCH2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LRCH2 Gene

InterPro:
Blocks:
  • Leucine-rich repeat signature
  • Calponin-like actin-binding

Suggested Antigen Peptide Sequences for LRCH2 Gene

GenScript: Design optimal peptide antigens:
  • LRCH2 protein (A4FVC3_HUMAN)
  • Leucine-rich repeat and calponin homology domain-containing protein 2 (LRCH2_HUMAN)
  • LRCH2 protein (Q08AD5_HUMAN)
genes like me logo Genes that share domains with LRCH2: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LRCH2 Gene

Function for LRCH2 Gene

Molecular function for LRCH2 Gene

UniProtKB/Swiss-Prot Function:
May play a role in the organization of the cytoskeleton.

Gene Ontology (GO) - Molecular Function for LRCH2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 24255178
genes like me logo Genes that share ontologies with LRCH2: view
genes like me logo Genes that share phenotypes with LRCH2: view

miRNA for LRCH2 Gene

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRCH2

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRCH2 Gene

Localization for LRCH2 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 LRCH2 gene
Compartment Confidence
nucleus 3
plasma membrane 2
cytosol 2
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Plasma membrane (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for LRCH2 Gene

Pathways & Interactions for LRCH2 Gene

PathCards logo

SuperPathways for LRCH2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRCH2 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for LRCH2 Gene

Drugs & Compounds for LRCH2 Gene

No Compound Related Data Available

Transcripts for LRCH2 Gene

mRNA/cDNA for LRCH2 Gene

2 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
2 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 LRCH2

Alternative Splicing Database (ASD) splice patterns (SP) for LRCH2 Gene

No ASD Table

Relevant External Links for LRCH2 Gene

GeneLoc Exon Structure for
LRCH2

Expression for LRCH2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRCH2 Gene

Protein differential expression in normal tissues from HIPED for LRCH2 Gene

This gene is overexpressed in Frontal cortex (33.5) and Adrenal (26.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LRCH2 Gene



Protein tissue co-expression partners for LRCH2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRCH2

SOURCE GeneReport for Unigene cluster for LRCH2 Gene:

Hs.65366
genes like me logo Genes that share expression patterns with LRCH2: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRCH2 Gene

Orthologs for LRCH2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRCH2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LRCH2 29 30
  • 96.75 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LRCH2 29 30
  • 94.82 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LRCH2 29
  • 94.04 (n)
Rat
(Rattus norvegicus)
Mammalia Lrch2 29
  • 90.64 (n)
Mouse
(Mus musculus)
Mammalia Lrch2 29 16 30
  • 90.56 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LRCH2 30
  • 86 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LRCH2 30
  • 68 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LRCH2 29 30
  • 80.3 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LRCH2 30
  • 69 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lrch2 29
  • 74.11 (n)
Str.4233 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.33837 29
Zebrafish
(Danio rerio)
Actinopterygii lrch2 30
  • 66 (a)
OneToOne
LOC101882684 29
  • 65.87 (n)
Species where no ortholog for LRCH2 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)
  • 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 LRCH2 Gene

ENSEMBL:
Gene Tree for LRCH2 (if available)
TreeFam:
Gene Tree for LRCH2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRCH2: view image
Alliance of Genome Resources:
Additional Orthologs for LRCH2

Paralogs for LRCH2 Gene

(4) SIMAP similar genes for LRCH2 Gene using alignment to 2 proteins:

  • LRCH2_HUMAN
  • A4FVC3_HUMAN
genes like me logo Genes that share paralogs with LRCH2: view

Variants for LRCH2 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LRCH2 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 LRCH2 Gene

Variant ID Type Subtype PubMed ID
esv1448157 CNV deletion 17803354
esv33994 CNV gain+loss 17666407
esv3452048 CNV insertion 20981092
esv3577049 CNV gain 25503493
esv3577051 CNV gain 25503493
nsv1075738 CNV deletion 25765185
nsv1118067 CNV deletion 24896259
nsv1153779 CNV duplication 26484159
nsv511667 CNV gain 21212237
nsv513764 CNV insertion 21212237
nsv516624 CNV gain 19592680
nsv520351 CNV gain 19592680

Variation tolerance for LRCH2 Gene

Gene Damage Index Score: 1.23; 24.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRCH2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRCH2
Leiden Open Variation Database (LOVD)
LRCH2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRCH2 Gene

Disorders for LRCH2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LRCH2 Gene - From: COP

Disorder Aliases PubMed IDs
hermansky-pudlak syndrome 3
  • hps3
separation anxiety disorder
  • separation anxiety disorder of childhood
- elite association - COSMIC cancer census association via MalaCards
Search LRCH2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LRCH2

genes like me logo Genes that share disorders with LRCH2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRCH2 Gene

Publications for LRCH2 Gene

  1. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10819331) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4
  2. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. (PMID: 33060197) Gordon DE … Krogan NJ (Science (New York, N.Y.) 2020) 3
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for LRCH2 Gene

Sources for LRCH2 Gene