Aliases for LRRC39 Gene

Aliases for LRRC39 Gene

  • Leucine Rich Repeat Containing 39 2 3 5
  • Myomasp 2 3 4
  • Myosin-Interacting M-Band-Associated Stress-Responsive Protein 3 4
  • Leucine-Rich Repeat-Containing Protein 39 3 4
  • Myosin-Interacting, M-Band-Associated Stress-Responsive Protein 2
  • Densin Hlg 3
  • MGC14816 2
  • LRRC39 5

External Ids for LRRC39 Gene

Previous GeneCards Identifiers for LRRC39 Gene

  • GC01M100327
  • GC01M100614
  • GC01M098737

Summaries for LRRC39 Gene

GeneCards Summary for LRRC39 Gene

LRRC39 (Leucine Rich Repeat Containing 39) is a Protein Coding gene. Diseases associated with LRRC39 include Myasthenic Syndrome, Congenital, 15 and Myopathy, Distal, 1. An important paralog of this gene is LRRC2.

UniProtKB/Swiss-Prot Summary for LRRC39 Gene

  • Component of the sarcomeric M-band which plays a role in myocyte response to biomechanical stress. May regulate expression of other M-band proteins via an SRF-dependent pathway. Important for normal contractile function in heart.

Gene Wiki entry for LRRC39 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRRC39 Gene

Genomics for LRRC39 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LRRC39 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
GH01J100178 Promoter/Enhancer 1.1 EPDnew Ensembl ENCODE 265.9 +0.8 772 2.2 RAD51 L3MBTL2 ZNF354B MEF2D LRRC39 SASS6 TRMT13 RTCA HNRNPA1P68 SLC30A7 MFSD14A SLC35A3 HSALNG0005515
GH01J100035 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 16.6 +140.0 139972 5 BCLAF1 MYC ZNF600 IKZF1 ZNF592 KLF9 POLR2A ZBTB10 YY1 NONO MFSD14A ENSG00000228084 SASS6 LRRC39 TRMT13 RTCA AGL ENSG00000283761
GH01J100046 Promoter/Enhancer 1.4 EPDnew FANTOM5 ENCODE 16 +129.8 129823 4.5 ZNF600 FOXA2 ZNF316 EBF1 NFE2 PRDM6 BHLHE40 SMARCA4 SPI1 NFE2L2 MFSD14A SASS6 LRRC39 HNRNPA1P68 TRMT13 RTCA FRRS1 ENSG00000228084 HSALNG0005502 ENSG00000283761
GH01J100028 Enhancer 0.9 FANTOM5 Ensembl ENCODE 16.6 +149.4 149362 1.4 ATF1 ZBTB33 NFATC1 ZNF362 CREM RUNX3 lnc-SLC35A3-1 LRRC39 RTCA FRRS1 CDC14A MFSD14A HSALNG0005499 ENSG00000228084 ENSG00000283761 SLC35A3
GH01J099943 Enhancer 1 Ensembl ENCODE 14.1 +234.5 234532 1.9 NCOR1 IKZF1 ZNF592 NFIC HES1 MNT ARNT TAF9B NBN TAL1 HSALNG0005494 LRRC39 SLC35A3 ENSG00000228084 FRRS1 MN308966 AGL
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRRC39 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRRC39

Top Transcription factor binding sites by QIAGEN in the LRRC39 gene promoter:
  • C/EBPalpha
  • Cart-1
  • GATA-1
  • Nkx2-2
  • POU3F2
  • RORalpha2
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c
  • STAT3

Genomic Locations for LRRC39 Gene

Latest Assembly
chr1:100,148,448-100,178,273
(GRCh38/hg38)
Size:
29,826 bases
Orientation:
Minus strand

Previous Assembly
chr1:100,614,004-100,643,812
(GRCh37/hg19 by Entrez Gene)
Size:
29,809 bases
Orientation:
Minus strand

chr1:100,614,409-100,643,771
(GRCh37/hg19 by Ensembl)
Size:
29,363 bases
Orientation:
Minus strand

Genomic View for LRRC39 Gene

Genes around LRRC39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRC39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRC39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRC39 Gene

Proteins for LRRC39 Gene

  • Protein details for LRRC39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96DD0-LRC39_HUMAN
    Recommended name:
    Leucine-rich repeat-containing protein 39
    Protein Accession:
    Q96DD0
    Secondary Accessions:
    • B3KUD2
    • D3DT56
    • Q5VVK7

    Protein attributes for LRRC39 Gene

    Size:
    335 amino acids
    Molecular mass:
    38793 Da
    Quaternary structure:
    • Interacts with MYH7 (via C-terminus).

    Alternative splice isoforms for LRRC39 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRRC39 Gene

Post-translational modifications for LRRC39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LRRC39 Gene

No data available for DME Specific Peptides for LRRC39 Gene

Domains & Families for LRRC39 Gene

Gene Families for LRRC39 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LRRC39 Gene

Suggested Antigen Peptide Sequences for LRRC39 Gene

GenScript: Design optimal peptide antigens:
  • Densin hlg (LRC39_HUMAN)
genes like me logo Genes that share domains with LRRC39: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LRRC39 Gene

Function for LRRC39 Gene

Molecular function for LRRC39 Gene

UniProtKB/Swiss-Prot Function:
Component of the sarcomeric M-band which plays a role in myocyte response to biomechanical stress. May regulate expression of other M-band proteins via an SRF-dependent pathway. Important for normal contractile function in heart.

Phenotypes From GWAS Catalog for LRRC39 Gene

Gene Ontology (GO) - Molecular Function for LRRC39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004722 protein serine/threonine phosphatase activity IBA 21873635
GO:0005515 protein binding IPI 20847312
genes like me logo Genes that share ontologies with LRRC39: view
genes like me logo Genes that share phenotypes with LRRC39: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRC39

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRRC39 Gene

Localization for LRRC39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRC39 Gene

Cytoplasm, myofibril, sarcomere, M line.

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 LRRC39 gene
Compartment Confidence
nucleus 3
cytosol 3
cytoskeleton 1
endoplasmic reticulum 1
mitochondrion 0

Gene Ontology (GO) - Cellular Components for LRRC39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
GO:0031430 M band IEA --
GO:0043231 intracellular membrane-bounded organelle IBA 21873635
genes like me logo Genes that share ontologies with LRRC39: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRRC39 Gene

Pathways & Interactions for LRRC39 Gene

PathCards logo

SuperPathways for LRRC39 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRRC39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IEA --
GO:0007165 signal transduction IBA 21873635
genes like me logo Genes that share ontologies with LRRC39: view

No data available for Pathways by source and SIGNOR curated interactions for LRRC39 Gene

Drugs & Compounds for LRRC39 Gene

No Compound Related Data Available

Transcripts for LRRC39 Gene

mRNA/cDNA for LRRC39 Gene

4 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
4 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 LRRC39

Alternative Splicing Database (ASD) splice patterns (SP) for LRRC39 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7
SP1: - -
SP2: -
SP3:

Relevant External Links for LRRC39 Gene

GeneLoc Exon Structure for
LRRC39

Expression for LRRC39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRRC39 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRRC39 Gene

This gene is overexpressed in Muscle - Skeletal (x17.4), Heart - Left Ventricle (x13.4), and Heart - Atrial Appendage (x7.2).

Protein differential expression in normal tissues from HIPED for LRRC39 Gene

This gene is overexpressed in Gallbladder (15.6), Plasma (14.7), Rectum (10.9), and Prostate (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LRRC39 Gene



Protein tissue co-expression partners for LRRC39 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRRC39

SOURCE GeneReport for Unigene cluster for LRRC39 Gene:

Hs.44277

mRNA Expression by UniProt/SwissProt for LRRC39 Gene:

Q96DD0-LRC39_HUMAN
Tissue specificity: Highly expressed in skeletal muscle and heart. Not detected in other tissues tested.

Evidence on tissue expression from TISSUES for LRRC39 Gene

  • Muscle(4.6)
  • Heart(2.7)
genes like me logo Genes that share expression patterns with LRRC39: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRC39 Gene

Orthologs for LRRC39 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRRC39 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LRRC39 29 30
  • 99.6 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LRRC39 29 30
  • 91.94 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LRRC39 29 30
  • 91.52 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lrrc39 29 16 30
  • 86.03 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lrrc39 29
  • 84.93 (n)
Oppossum
(Monodelphis domestica)
Mammalia LRRC39 30
  • 82 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LRRC39 30
  • 80 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LRRC39 29 30
  • 69.85 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LRRC39 30
  • 68 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lrrc39 29
  • 61.17 (n)
Zebrafish
(Danio rerio)
Actinopterygii lrrc39 29 30
  • 63.43 (n)
OneToOne
Species where no ortholog for LRRC39 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)
  • 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 LRRC39 Gene

ENSEMBL:
Gene Tree for LRRC39 (if available)
TreeFam:
Gene Tree for LRRC39 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRRC39: view image
Alliance of Genome Resources:
Additional Orthologs for LRRC39

Paralogs for LRRC39 Gene

(2) SIMAP similar genes for LRRC39 Gene using alignment to 1 proteins:

  • LRC39_HUMAN
genes like me logo Genes that share paralogs with LRRC39: view

Variants for LRRC39 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRRC39 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs80221535 Benign: not provided 100,159,391(-) G/A
NM_001256385.1(LRRC39):c.244C>T (p.Leu82=)
SYNONYMOUS
rs34920283 -- p.Ile121Leu

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LRRC39 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 LRRC39 Gene

Variant ID Type Subtype PubMed ID
nsv2121 CNV insertion 18451855
nsv830804 CNV gain 17160897

Variation tolerance for LRRC39 Gene

Residual Variation Intolerance Score: 72.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.28; 62.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRC39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRC39
Leiden Open Variation Database (LOVD)
LRRC39

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRC39 Gene

Disorders for LRRC39 Gene

MalaCards: The human disease database

(5) MalaCards diseases for LRRC39 Gene - From: COP

Disorder Aliases PubMed IDs
myasthenic syndrome, congenital, 15
  • cms15
myopathy, distal, 1
  • mpd1
lateral meningocele syndrome
  • lmns
jalili syndrome
  • cone-rod dystrophy and amelogenesis imperfecta
cardiomyopathy, familial hypertrophic, 1
  • cmh1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LRRC39

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 LRRC39: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRRC39 Gene

Publications for LRRC39 Gene

  1. Myomasp/LRRC39, a heart- and muscle-specific protein, is a novel component of the sarcomeric M-band and is involved in stretch sensing. (PMID: 20847312) Will RD … Frey N (Circulation research 2010) 2 3 4
  2. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for LRRC39 Gene

Sources for LRRC39 Gene