Aliases for LRRC40 Gene

Aliases for LRRC40 Gene

  • Leucine Rich Repeat Containing 40 2 3 5
  • Leucine-Rich Repeat-Containing Protein 40 3 4
  • Testicular Tissue Protein Li 109 3
  • DJ677H15.1 3

External Ids for LRRC40 Gene

Previous GeneCards Identifiers for LRRC40 Gene

  • GC01M070323
  • GC01M070610
  • GC01M068721

Summaries for LRRC40 Gene

GeneCards Summary for LRRC40 Gene

LRRC40 (Leucine Rich Repeat Containing 40) is a Protein Coding gene. An important paralog of this gene is LRRD1.

Gene Wiki entry for LRRC40 Gene

Additional gene information for LRRC40 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRRC40 Gene

Genomics for LRRC40 Gene

GeneHancer (GH) Regulatory Elements for LRRC40 Gene

Promoters and enhancers for LRRC40 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
GH01J070203 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 506.3 -0.2 -202 4.3 ZBTB40 ZNF217 EP300 TCF12 SIN3A MYC NRF1 POLR2G SP1 NCOR1 LRRC40 SRSF11 piR-34911-001
GH01J070219 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 5.9 -16.2 -16187 4.3 HNRNPK EP300 ZSCAN5C NRF1 POLR2G GTF2E2 PHF8 ZFX ZNF10 ZIC2 ENSG00000228988 NONHSAG001792.2-001 SRSF11 LRRC40 lnc-LRRC7-5
GH01J070504 Enhancer 1.1 Ensembl ENCODE 11.8 -298.7 -298723 2.8 JUND ZNF639 EP300 REST TRIM28 RCOR1 TRIM22 OSR2 BCL11A FOXA2 LRRC40 ANKRD13C ZRANB2 MIR186 lnc-ANKRD13C-3 CHORDC1P5 lnc-CTH-11
GH01J070156 Enhancer 0.8 Ensembl 11.3 +48.9 48878 0.4 AFF1 TOE1 CTBP1 JUN NEUROD1 ZNF316 FOSL1 FOSL2 PBX2 JUND LRRC40 SRSF11 lnc-LRRC7-2 lnc-ANKRD13C-2 RF00017-244 RN7SL242P
GH01J070352 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 4.2 -148.3 -148323 4.8 ZBTB40 ZNF217 EP300 TCF12 SIN3A NRF1 POLR2G GTF2E2 PHF8 TEAD4 HHLA3 ANKRD13C SRSF11 ZRANB2 MIR186 LRRC40 HHLA3-AS1 lnc-LRRC40-5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRRC40 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRRC40

Top Transcription factor binding sites by QIAGEN in the LRRC40 gene promoter:
  • CREB
  • deltaCREB
  • E2F-4
  • E2F-5
  • FOXL1
  • GATA-1
  • GATA-2
  • GATA-3
  • HNF-3beta
  • POU6F1 (c2)

Genomic Locations for LRRC40 Gene

Genomic Locations for LRRC40 Gene
chr1:70,144,802-70,205,678
(GRCh38/hg38)
Size:
60,877 bases
Orientation:
Minus strand
chr1:70,610,485-70,671,361
(GRCh37/hg19)
Size:
60,877 bases
Orientation:
Minus strand

Genomic View for LRRC40 Gene

Genes around LRRC40 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRC40 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRC40 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRC40 Gene

Proteins for LRRC40 Gene

  • Protein details for LRRC40 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H9A6-LRC40_HUMAN
    Recommended name:
    Leucine-rich repeat-containing protein 40
    Protein Accession:
    Q9H9A6
    Secondary Accessions:
    • Q9BTR7
    • Q9NSK1
    • Q9NXC1

    Protein attributes for LRRC40 Gene

    Size:
    602 amino acids
    Molecular mass:
    68250 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA91094.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for LRRC40 Gene

Post-translational modifications for LRRC40 Gene

  • Ubiquitination at Lys86 and Lys93
  • Modification sites at PhosphoSitePlus

Other Protein References for LRRC40 Gene

No data available for DME Specific Peptides for LRRC40 Gene

Domains & Families for LRRC40 Gene

Gene Families for LRRC40 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LRRC40 Gene

Suggested Antigen Peptide Sequences for LRRC40 Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich repeat-containing protein 40 (LRC40_HUMAN)
genes like me logo Genes that share domains with LRRC40: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LRRC40 Gene

Function for LRRC40 Gene

Phenotypes From GWAS Catalog for LRRC40 Gene

genes like me logo Genes that share phenotypes with LRRC40: view

Animal Model Products

CRISPR Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRRC40 Gene

Localization for LRRC40 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 LRRC40 gene
Compartment Confidence
nucleus 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LRRC40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with LRRC40: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for LRRC40 Gene

Pathways & Interactions for LRRC40 Gene

PathCards logo

SuperPathways for LRRC40 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRRC40 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for LRRC40 Gene

Drugs & Compounds for LRRC40 Gene

No Compound Related Data Available

Transcripts for LRRC40 Gene

mRNA/cDNA for LRRC40 Gene

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

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRRC40 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16
SP1: -
SP2: - -
SP3: - - -
SP4: - -

Relevant External Links for LRRC40 Gene

GeneLoc Exon Structure for
LRRC40

Expression for LRRC40 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRRC40 Gene

Protein differential expression in normal tissues from HIPED for LRRC40 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.8), Fetal Brain (8.7), and Brain (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LRRC40 Gene



Protein tissue co-expression partners for LRRC40 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRRC40

SOURCE GeneReport for Unigene cluster for LRRC40 Gene:

Hs.147836

Evidence on tissue expression from TISSUES for LRRC40 Gene

  • Nervous system(2.9)
genes like me logo Genes that share expression patterns with LRRC40: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRC40 Gene

Orthologs for LRRC40 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LRRC40 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRRC40 31 30
  • 99.61 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LRRC40 31 30
  • 89.37 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LRRC40 31 30
  • 89.23 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lrrc40 17 31 30
  • 82.34 (n)
rat
(Rattus norvegicus)
Mammalia Lrrc40 30
  • 81.44 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LRRC40 31
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LRRC40 31
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves LRRC40 31 30
  • 69.71 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LRRC40 31
  • 60 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrc40 30
  • 63.95 (n)
zebrafish
(Danio rerio)
Actinopterygii lrrc40 31 30
  • 61.17 (n)
OneToOne
-- 30
fruit fly
(Drosophila melanogaster)
Insecta f-cup 31 30
  • 45.77 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006993 30
  • 45.4 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G15410 30
  • 44.18 (n)
rice
(Oryza sativa)
Liliopsida Os02g0826600 30
  • 44.97 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05545 30
  • 41.42 (n)
Species where no ortholog for LRRC40 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LRRC40 Gene

ENSEMBL:
Gene Tree for LRRC40 (if available)
TreeFam:
Gene Tree for LRRC40 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRRC40: view image

Paralogs for LRRC40 Gene

(2) SIMAP similar genes for LRRC40 Gene using alignment to 1 proteins:

  • LRC40_HUMAN

Pseudogenes.org Pseudogenes for LRRC40 Gene

genes like me logo Genes that share paralogs with LRRC40: view

Variants for LRRC40 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRRC40 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs270495 - p.Gln53Pro
rs3180401 - p.Ile500Val

Additional dbSNP identifiers (rs#s) for LRRC40 Gene

Structural Variations from Database of Genomic Variants (DGV) for LRRC40 Gene

Variant ID Type Subtype PubMed ID
esv2665402 CNV deletion 23128226
esv3586350 CNV loss 21293372
nsv1005397 CNV gain 25217958
nsv1076523 CNV deletion 25765185
nsv1343 CNV insertion 18451855
nsv823143 CNV loss 20364138

Variation tolerance for LRRC40 Gene

Residual Variation Intolerance Score: 88.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.72; 46.50% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRC40 Gene

Human Gene Mutation Database (HGMD)
LRRC40
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRC40

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRC40 Gene

Disorders for LRRC40 Gene

Additional Disease Information for LRRC40

No disorders were found for LRRC40 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRRC40 Gene

Publications for LRRC40 Gene

  1. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 54
  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 54
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  4. 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 54
  5. Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function. (PMID: 29467282) Heidelberger JB … Beli P (EMBO reports 2018) 3 54

Products for LRRC40 Gene

Sources for LRRC40 Gene