Aliases for LRRC56 Gene

Aliases for LRRC56 Gene

  • Leucine Rich Repeat Containing 56 2 3 5
  • Leucine-Rich Repeat-Containing Protein 56 3 4
  • DKFZp761L1518 2
  • FLJ00101 2
  • CILD39 3
  • LRRC56 5

External Ids for LRRC56 Gene

Previous GeneCards Identifiers for LRRC56 Gene

  • GC11P000529
  • GC11P000537
  • GC11P000352
  • GC11P000520

Summaries for LRRC56 Gene

GeneCards Summary for LRRC56 Gene

LRRC56 (Leucine Rich Repeat Containing 56) is a Protein Coding gene. Diseases associated with LRRC56 include Ciliary Dyskinesia, Primary, 39 and Primary Ciliary Dyskinesia.

UniProtKB/Swiss-Prot Summary for LRRC56 Gene

Additional gene information for LRRC56 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRRC56 Gene

Genomics for LRRC56 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LRRC56 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRRC56 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRRC56

Top Transcription factor binding sites by QIAGEN in the LRRC56 gene promoter:
  • HEN1
  • NF-1
  • NF-1/L
  • NF-kappaB1
  • Pax-2
  • Pax-2a
  • TGIF

Genomic Locations for LRRC56 Gene

Genomic Locations for LRRC56 Gene
chr11:518,967-554,916
(GRCh38/hg38)
Size:
35,950 bases
Orientation:
Plus strand
chr11:537,522-554,916
(GRCh37/hg19)
Size:
17,395 bases
Orientation:
Plus strand

Genomic View for LRRC56 Gene

Genes around LRRC56 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRC56 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRC56 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRC56 Gene

Proteins for LRRC56 Gene

  • Protein details for LRRC56 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IYG6-LRC56_HUMAN
    Recommended name:
    Leucine-rich repeat-containing protein 56
    Protein Accession:
    Q8IYG6
    Secondary Accessions:
    • Q8N3Q4

    Protein attributes for LRRC56 Gene

    Size:
    542 amino acids
    Molecular mass:
    58733 Da
    Quaternary structure:
    • Interacts with IFT88.

neXtProt entry for LRRC56 Gene

Post-translational modifications for LRRC56 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LRRC56 Gene

Domains & Families for LRRC56 Gene

Gene Families for LRRC56 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LRRC56 Gene

InterPro:
Blocks:
  • Leucine-rich repeat signature
  • Leucine-rich-associated
ProtoNet:

Suggested Antigen Peptide Sequences for LRRC56 Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich repeat-containing protein 56 (LRC56_HUMAN)
  • LRRC56 protein (Q0P6F0_HUMAN)
  • FLJ00101 protein (Q9H7I5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IYG6

UniProtKB/Swiss-Prot:

LRC56_HUMAN :
  • Belongs to the LRRC56 family.
Family:
  • Belongs to the LRRC56 family.
genes like me logo Genes that share domains with LRRC56: view

Function for LRRC56 Gene

Molecular function for LRRC56 Gene

UniProtKB/Swiss-Prot Function:
Required for the assembly of dynein arms.

Phenotypes From GWAS Catalog for LRRC56 Gene

Gene Ontology (GO) - Molecular Function for LRRC56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 30388400
genes like me logo Genes that share ontologies with LRRC56: view
genes like me logo Genes that share phenotypes with LRRC56: view

Human Phenotype Ontology for LRRC56 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRC56

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LRRC56 Gene

Localization for LRRC56 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRC56 Gene

Cell projection, cilium.

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 LRRC56 gene
Compartment Confidence
nucleus 2
cytosol 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for LRRC56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005929 cilium IEA --
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with LRRC56: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRRC56 Gene

Pathways & Interactions for LRRC56 Gene

PathCards logo

SuperPathways for LRRC56 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRRC56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030030 cell projection organization IEA --
genes like me logo Genes that share ontologies with LRRC56: view

No data available for Pathways by source and SIGNOR curated interactions for LRRC56 Gene

Drugs & Compounds for LRRC56 Gene

No Compound Related Data Available

Transcripts for LRRC56 Gene

mRNA/cDNA for LRRC56 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRC56

Alternative Splicing Database (ASD) splice patterns (SP) for LRRC56 Gene

No ASD Table

Relevant External Links for LRRC56 Gene

GeneLoc Exon Structure for
LRRC56

Expression for LRRC56 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRRC56 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)

mRNA differential expression in normal tissues according to GTEx for LRRC56 Gene

This gene is overexpressed in Testis (x8.2) and Pituitary (x5.5).

Protein differential expression in normal tissues from HIPED for LRRC56 Gene

This gene is overexpressed in Tlymphocyte (27.9), Plasma (21.4), Brain (11.4), and Heart (8.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LRRC56 Gene



Protein tissue co-expression partners for LRRC56 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRRC56

SOURCE GeneReport for Unigene cluster for LRRC56 Gene:

Hs.567655

Evidence on tissue expression from TISSUES for LRRC56 Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with LRRC56: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRC56 Gene

Orthologs for LRRC56 Gene

This gene was present in the common ancestor of animals.

Orthologs for LRRC56 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LRRC56 30 31
  • 98.34 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lrrc56 30 17 31
  • 79.07 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LRRC56 30 31
  • 79.02 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LRRC56 30 31
  • 78.3 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lrrc56 30
  • 77.89 (n)
Oppossum
(Monodelphis domestica)
Mammalia LRRC56 31
  • 40 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LRRC56 31
  • 53 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LRRC56 31
  • 51 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii LRRC56 (1 of 2) 31
  • 51 (a)
OneToMany
LRRC56 (2 of 2) 31
  • 36 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta CG14185 31
  • 24 (a)
OneToOne
Species where no ortholog for LRRC56 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for LRRC56 Gene

ENSEMBL:
Gene Tree for LRRC56 (if available)
TreeFam:
Gene Tree for LRRC56 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRRC56: view image

Paralogs for LRRC56 Gene

(1) SIMAP similar genes for LRRC56 Gene using alignment to 2 proteins:

  • LRC56_HUMAN
  • Q0P6F0_HUMAN
genes like me logo Genes that share paralogs with LRRC56: view

No data available for Paralogs for LRRC56 Gene

Variants for LRRC56 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRRC56 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
639168 Uncertain Significance: Costello syndrome 533,521(+) G/A MISSENSE_VARIANT,SYNONYMOUS_VARIANT
643338 Uncertain Significance: Costello syndrome 532,686(+) G/C MISSENSE_VARIANT,THREE_PRIME_UTR_VARIANT
644041 Uncertain Significance: Costello syndrome 532,725(+) G/A MISSENSE_VARIANT,THREE_PRIME_UTR_VARIANT
647934 Uncertain Significance: Costello syndrome 533,757(+) G/C INTRON_VARIANT
648589 Uncertain Significance: Costello syndrome 532,758(+) G/A INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for LRRC56 Gene

Structural Variations from Database of Genomic Variants (DGV) for LRRC56 Gene

Variant ID Type Subtype PubMed ID
dgv182e199 CNV deletion 23128226
dgv564n106 OTHER inversion 24896259
esv2743844 CNV deletion 23290073
esv2759794 CNV loss 17122850
esv3625069 CNV loss 21293372
esv3625070 CNV loss 21293372
nsv1039558 CNV gain 25217958
nsv1053964 CNV gain 25217958
nsv1077764 OTHER inversion 25765185
nsv1159791 CNV deletion 26073780
nsv467634 CNV loss 19166990
nsv469923 CNV loss 18288195
nsv469924 CNV gain 18288195
nsv527327 CNV loss 19592680
nsv552854 CNV loss 21841781
nsv552855 CNV loss 21841781
nsv552856 CNV gain 21841781
nsv951270 CNV deletion 24416366

Variation tolerance for LRRC56 Gene

Residual Variation Intolerance Score: 94.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.19; 75.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRC56 Gene

Human Gene Mutation Database (HGMD)
LRRC56
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRC56

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRC56 Gene

Disorders for LRRC56 Gene

MalaCards: The human disease database

(15) MalaCards diseases for LRRC56 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
ciliary dyskinesia, primary, 39
  • cild39
primary ciliary dyskinesia
  • pcd
breast squamous cell carcinoma
  • breast primary squamous cell carcinoma
large congenital melanocytic nevus
  • melanocytic nevus syndrome, congenital
spitz nevus
  • spitz naevus
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

LRC56_HUMAN
  • Ciliary dyskinesia, primary, 39 (CILD39) [MIM:618254]: A form of primary ciliary dyskinesia, a disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia. Some patients exhibit randomization of left-right body asymmetry and situs inversus. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. CILD39 inheritance is autosomal recessive. {ECO:0000269 PubMed:30388400}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with LRRC56: view

No data available for Genatlas for LRRC56 Gene

Publications for LRRC56 Gene

  1. Biallelic Mutations in LRRC56, Encoding a Protein Associated with Intraflagellar Transport, Cause Mucociliary Clearance and Laterality Defects. (PMID: 30388400) Bonnefoy S … Sheridan EG (American journal of human genetics 2018) 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3

Products for LRRC56 Gene

Sources for LRRC56 Gene