Aliases for LYPD1 Gene

Aliases for LYPD1 Gene

  • LY6/PLAUR Domain Containing 1 2 3 5
  • Ly6/PLAUR Domain-Containing Protein 1 3 4
  • Putative HeLa Tumor Suppressor 3 4
  • LYPDC1 3 4
  • PHTS 3 4
  • MGC29643 2
  • LYPD1 5

External Ids for LYPD1 Gene

Previous HGNC Symbols for LYPD1 Gene

  • LYPDC1

Previous GeneCards Identifiers for LYPD1 Gene

  • GC02M133238
  • GC02M133118
  • GC02M133402
  • GC02M125395

Summaries for LYPD1 Gene

GeneCards Summary for LYPD1 Gene

LYPD1 (LY6/PLAUR Domain Containing 1) is a Protein Coding gene. Diseases associated with LYPD1 include Progesterone-Receptor Positive Breast Cancer and Acute Stress Disorder. Among its related pathways are Metabolism of proteins and Post-translational modification- synthesis of GPI-anchored proteins. An important paralog of this gene is LYPD2.

UniProtKB/Swiss-Prot Summary for LYPD1 Gene

  • Believed to act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro increases receptor desensitization and decreases affinity for ACh of alpha-4:beta-2-containing nAChRs. May play a role in the intracellular trafficking of alpha-4:beta-2 and alpha-7-containing nAChRs and may inhibit their expression at the cell surface. May be involved in the control of anxiety.

Gene Wiki entry for LYPD1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LYPD1 Gene

Genomics for LYPD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LYPD1 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
GH02J132669 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 250.7 +1.4 1421 3.9 ZBTB10 FEZF1 ZEB1 CTCF ZIC2 CEBPB MAX EP300 ZNF341 SP2 HSALNG0018983 LYPD1 ENSG00000230065 LOC105373623 GPR39
GH02J132645 Enhancer 0.5 Ensembl 16 +25.4 25379 1.6 SPI1 FOXA1 NRF1 L3MBTL2 SP1 GATA2 RXRA MGA LYPD1 LOC105373623 lnc-GPR39-5 GPR39
GH02J132702 Enhancer 0.3 Ensembl 11.3 -30.5 -30522 0.2 JUND FOS LYPD1 ENSG00000230065 ENSG00000286068 piR-43107-161 NCKAP5
GH02J132815 Enhancer 0.7 Ensembl ENCODE 4.3 -144.4 -144422 1.6 BRCA1 CEBPB EP300 RFX5 YY1 NFE2 MAFK CREB1 BACH1 FOS LYPD1 lnc-LYPD1-2 HSALNG0018986 ENSG00000286068 NCKAP5
GH02J132447 Enhancer 0.6 FANTOM5 Ensembl 1.8 +224.9 224898 1 SPI1 TRIM22 FOXK2 RNU6-175P LYPD1 MIR9986 GPR39 lnc-LYPD1-3 lnc-GPR39-10
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LYPD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LYPD1

Top Transcription factor binding sites by QIAGEN in the LYPD1 gene promoter:
  • CUTL1
  • Evi-1
  • HTF
  • p53
  • SRF

Genomic Locations for LYPD1 Gene

Latest Assembly
chr2:132,643,286-132,671,579
(GRCh38/hg38)
Size:
28,294 bases
Orientation:
Minus strand

Previous Assembly
chr2:133,400,859-133,429,099
(GRCh37/hg19 by Entrez Gene)
Size:
28,241 bases
Orientation:
Minus strand

chr2:133,402,426-133,429,152
(GRCh37/hg19 by Ensembl)
Size:
26,727 bases
Orientation:
Minus strand

Genomic View for LYPD1 Gene

Genes around LYPD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LYPD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LYPD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LYPD1 Gene

Proteins for LYPD1 Gene

  • Protein details for LYPD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N2G4-LYPD1_HUMAN
    Recommended name:
    Ly6/PLAUR domain-containing protein 1
    Protein Accession:
    Q8N2G4
    Secondary Accessions:
    • H7BXW6
    • Q6ZP52
    • Q6ZWI4
    • Q96AC2

    Protein attributes for LYPD1 Gene

    Size:
    141 amino acids
    Molecular mass:
    15240 Da
    Quaternary structure:
    • Interacts with CHRNA4 and nAChRs containing alpha-4:beta-2 (CHRNA4:CHRNB2) and alpha-7 (CHRNA7) subunits.
    SequenceCaution:
    • Sequence=BAC11647.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for LYPD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LYPD1 Gene

Post-translational modifications for LYPD1 Gene

  • Glycosylation at Asn45
  • Modification sites at PhosphoSitePlus

Other Protein References for LYPD1 Gene

No data available for DME Specific Peptides for LYPD1 Gene

Domains & Families for LYPD1 Gene

Gene Families for LYPD1 Gene

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

Protein Domains for LYPD1 Gene

Blocks:
  • CD59 antigen
ProtoNet:

Suggested Antigen Peptide Sequences for LYPD1 Gene

GenScript: Design optimal peptide antigens:
  • LY6/PLAUR domain containing 1, isoform CRA_b (D3DP69_HUMAN)
  • Putative HeLa tumor suppressor (LYPD1_HUMAN)
  • LYPDC1 protein (Q8IXM0_HUMAN)
genes like me logo Genes that share domains with LYPD1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LYPD1 Gene

Function for LYPD1 Gene

Molecular function for LYPD1 Gene

UniProtKB/Swiss-Prot Function:
Believed to act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro increases receptor desensitization and decreases affinity for ACh of alpha-4:beta-2-containing nAChRs. May play a role in the intracellular trafficking of alpha-4:beta-2 and alpha-7-containing nAChRs and may inhibit their expression at the cell surface. May be involved in the control of anxiety.

Phenotypes From GWAS Catalog for LYPD1 Gene

Gene Ontology (GO) - Molecular Function for LYPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030550 acetylcholine receptor inhibitor activity IBA 21873635
genes like me logo Genes that share ontologies with LYPD1: view
genes like me logo Genes that share phenotypes with LYPD1: view

Animal Models for LYPD1 Gene

MGI Knock Outs for LYPD1:

Animal Models for research

  • Taconic Biosciences Mouse Models for LYPD1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LYPD1

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LYPD1 Gene

Localization for LYPD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LYPD1 Gene

Cell membrane. Lipid-anchor, GPI-anchor.

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 LYPD1 gene
Compartment Confidence
extracellular 5
plasma membrane 4
nucleus 2
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for LYPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0031225 anchored component of membrane IEA --
GO:0045202 synapse IEA --
genes like me logo Genes that share ontologies with LYPD1: view

Pathways & Interactions for LYPD1 Gene

genes like me logo Genes that share pathways with LYPD1: view

Gene Ontology (GO) - Biological Process for LYPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0095500 acetylcholine receptor signaling pathway IBA 21873635
GO:2000272 negative regulation of signaling receptor activity IEA --
genes like me logo Genes that share ontologies with LYPD1: view

No data available for SIGNOR curated interactions for LYPD1 Gene

Drugs & Compounds for LYPD1 Gene

No Compound Related Data Available

Transcripts for LYPD1 Gene

mRNA/cDNA for LYPD1 Gene

4 REFSEQ mRNAs :
19 NCBI additional mRNA sequence :
3 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 LYPD1

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for LYPD1 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e ^ 3a · 3b ^ 4a · 4b · 4c ^ 5a · 5b · 5c · 5d ^ 6a · 6b · 6c · 6d
SP1: - - - - - - - - -
SP2: - - - - - - - - - - - - -
SP3: - - - - - - - - -
SP4: - - - - -
SP5: - - - - - - - -
SP6: - -
SP7: -
SP8:
SP9: - - - -
SP10: - - - - - - -
SP11: - - -

Relevant External Links for LYPD1 Gene

GeneLoc Exon Structure for
LYPD1

Expression for LYPD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LYPD1 Gene

mRNA differential expression in normal tissues according to GTEx for LYPD1 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x7.2), Brain - Caudate (basal ganglia) (x5.3), Brain - Putamen (basal ganglia) (x4.4), Brain - Hypothalamus (x4.4), Pituitary (x4.2), and Brain - Hippocampus (x4.1).

Protein differential expression in normal tissues from HIPED for LYPD1 Gene

This gene is overexpressed in Fetal Brain (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LYPD1 Gene



Protein tissue co-expression partners for LYPD1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LYPD1

SOURCE GeneReport for Unigene cluster for LYPD1 Gene:

Hs.432395

Evidence on tissue expression from TISSUES for LYPD1 Gene

  • Nervous system(4.9)
  • Kidney(4.3)
  • Pancreas(4.2)
genes like me logo Genes that share expression patterns with LYPD1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LYPD1 Gene

Orthologs for LYPD1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LYPD1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LYPD1 30 31
  • 99.76 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LYPD1 30 31
  • 91.02 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LYPD1 30 31
  • 89.83 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lypd1 30 17 31
  • 89.6 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lypd1 30
  • 87.94 (n)
Oppossum
(Monodelphis domestica)
Mammalia LYPD1 31
  • 86 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LYPD1 30 31
  • 76.36 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LYPD1 31
  • 77 (a)
OneToOne
Species where no ortholog for LYPD1 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)
  • 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)
  • Zebrafish (Danio rerio)

Evolution for LYPD1 Gene

ENSEMBL:
Gene Tree for LYPD1 (if available)
TreeFam:
Gene Tree for LYPD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LYPD1: view image

Paralogs for LYPD1 Gene

Paralogs for LYPD1 Gene

(1) SIMAP similar genes for LYPD1 Gene using alignment to 3 proteins:

  • LYPD1_HUMAN
  • D3DP69_HUMAN
  • F8WD77_HUMAN
genes like me logo Genes that share paralogs with LYPD1: view

Variants for LYPD1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LYPD1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs10631541 Benign: not provided 132,645,507(-) T/TAAG
NM_001508.3(GPR39):c.1264_1266dup (p.Lys422dup)
INFRAME_INSERTION,THREE_PRIME_UTR
rs151118262 Benign: not provided 132,645,123(-) C/A
NM_001508.3(GPR39):c.879C>A (p.Ala293=)
SYNONYMOUS_VARIANT,THREE_PRIME_UTR
rs61735719 Conflicting Interpretations: not specified; not provided 132,645,376(-) G/A
NM_001508.3(GPR39):c.1132G>A (p.Ala378Thr)
MISSENSE_VARIANT,THREE_PRIME_UTR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LYPD1 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 LYPD1 Gene

Variant ID Type Subtype PubMed ID
esv4378 OTHER complex 18987735
nsv1011421 CNV gain 25217958
nsv583152 CNV gain 21841781
nsv583155 CNV loss 21841781
nsv583158 CNV gain 21841781

Variation tolerance for LYPD1 Gene

Residual Variation Intolerance Score: 51.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.64; 13.61% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LYPD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LYPD1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LYPD1 Gene

Disorders for LYPD1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LYPD1 Gene - From: COP

Disorder Aliases PubMed IDs
progesterone-receptor positive breast cancer
acute stress disorder
  • traumatic stress disorder
- elite association - COSMIC cancer census association via MalaCards
Search LYPD1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LYPD1

Genetic Association Database
(GAD)
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 LYPD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LYPD1 Gene

Publications for LYPD1 Gene

  1. 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 41
  2. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. (PMID: 16303743) Otsuki T … Isogai T (DNA research : an international journal for rapid publication of reports on genes and genomes 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. 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
  5. 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) 3 4

Products for LYPD1 Gene

Sources for LYPD1 Gene