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    LYPD6 LY6/PLAUR domain containing 6 [ Homo sapiens (human) ]

    Gene ID: 130574, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LYPD6provided by HGNC
    Official Full Name
    LY6/PLAUR domain containing 6provided by HGNC
    Primary source
    HGNC:HGNC:28751
    See related
    Ensembl:ENSG00000187123 MIM:613359; AllianceGenome:HGNC:28751
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Members of the LY6 protein family (see SLURP1; MIM 606119), such as LYPD6, have at least one 80-amino acid LU domain that contains 10 conserved cysteines with a defined disulfide-bonding pattern (Zhang et al., 2010 [PubMed 19653121]).[supplied by OMIM, Apr 2010]
    Expression
    Biased expression in gall bladder (RPKM 7.3), placenta (RPKM 6.8) and 12 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LYPD6 in Genome Data Viewer
    Location:
    2q23.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (149329985..149486378)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (149780390..149936801)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (150186499..150330652)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373679 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12004 Neighboring gene family with sequence similarity 8 member A3, pseudogene Neighboring gene uncharacterized LOC124906190 Neighboring gene microRNA 9899 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:150274403-150274924 Neighboring gene NANOG hESC enhancer GRCh37_chr2:150306659-150307199 Neighboring gene ribosomal protein L17 pseudogene 13 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:150363112-150363636 Neighboring gene Sharpr-MPRA regulatory region 14986 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:150443500-150444699 Neighboring gene MMADHC divergent transcript Neighboring gene metabolism of cobalamin associated D Neighboring gene RNA, U6 small nuclear 601, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Human Three-Finger Protein Lypd6 Is a Negative Modulator of the Cholinergic System in the Brain. Kulbatskii D, et al. Front Cell Dev Biol, 2021. PMID 34631692, Free PMC Article
    2. Identification and characterization of human LYPD6, a new member of the Ly-6 superfamily. Zhang Y, et al. Mol Biol Rep, 2010 Apr. PMID 19653121
    3. Structure of the Wnt signaling enhancer LYPD6 and its interactions with the Wnt coreceptor LRP6. Zhao Y, et al. FEBS Lett, 2018 Sep. PMID 30069874
    4. Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors. Paramonov AS, et al. Int J Mol Sci, 2020 Oct 1. PMID 33019770, Free PMC Article
    5. Functional interaction between Lypd6 and nicotinic acetylcholine receptors. Arvaniti M, et al. J Neurochem, 2016 Sep. PMID 27344019, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors.
      Title: Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors.
    2. Results indicate the key role in the interaction of LY6/PLAUR domain containing 6 (LYPD6) with LDL receptor related protein 6 (LRP6).
      Title: Structure of the Wnt signaling enhancer LYPD6 and its interactions with the Wnt coreceptor LRP6.
    3. the Lynx protein Lypd6 binds to nAChRs in human brain extracts, and that recombinant Lypd6 decreases nicotine-induced ERK phosphorylation
      Title: Functional interaction between Lypd6 and nicotinic acetylcholine receptors.
    4. Lypd6 appears to control Lrp6 activation specifically in membrane rafts, which is essential for downstream signaling.
      Title: Lypd6 enhances Wnt/β-catenin signaling by promoting Lrp6 phosphorylation in raft plasma membrane domains.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    6. The cloning and characterization of a novel human LU domain containing gene, LYPD6, isolated from human testis cDNA library, is reported.
      Title: Identification and characterization of human LYPD6, a new member of the Ly-6 superfamily.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC52057

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables acetylcholine receptor inhibitor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables acetylcholine receptor inhibitor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of canonical Wnt signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane raft IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ly6/PLAUR domain-containing protein 6

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001195685.2 → NP_001182614.1  ly6/PLAUR domain-containing protein 6 precursor

      See identical proteins and their annotated locations for NP_001182614.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC007394
      Consensus CDS
      CCDS2188.1
      UniProtKB/Swiss-Prot
      B3KWC0, Q4G121, Q53TR3, Q659B1, Q86Y78
      Related
      ENSP00000386413.1, ENST00000409381.5
      Conserved Domains (1) summary
      pfam16975
      Location:41 → 145
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    2. NM_194317.5 → NP_919298.1  ly6/PLAUR domain-containing protein 6 precursor

      See identical proteins and their annotated locations for NP_919298.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses a different segment for its 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC007394
      Consensus CDS
      CCDS2188.1
      UniProtKB/Swiss-Prot
      B3KWC0, Q4G121, Q53TR3, Q659B1, Q86Y78
      Related
      ENSP00000334463.4, ENST00000334166.9
      Conserved Domains (1) summary
      pfam16975
      Location:41 → 145
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      149329985..149486378
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024452699.2 → XP_024308467.1  ly6/PLAUR domain-containing protein 6 isoform X1

      UniProtKB/Swiss-Prot
      B3KWC0, Q4G121, Q53TR3, Q659B1, Q86Y78
      Related
      ENSP00000498455.1, ENST00000651933.1
      Conserved Domains (1) summary
      pfam16975
      Location:41 → 145
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    2. XM_024452701.2 → XP_024308469.1  ly6/PLAUR domain-containing protein 6 isoform X1

      UniProtKB/Swiss-Prot
      B3KWC0, Q4G121, Q53TR3, Q659B1, Q86Y78
      Conserved Domains (1) summary
      pfam16975
      Location:41 → 145
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    3. XM_047443400.1 → XP_047299356.1  ly6/PLAUR domain-containing protein 6 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      149780390..149936801
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340547.1 → XP_054196522.1  ly6/PLAUR domain-containing protein 6 isoform X1

      UniProtKB/Swiss-Prot
      B3KWC0, Q4G121, Q53TR3, Q659B1, Q86Y78

    2. XM_054340548.1 → XP_054196523.1  ly6/PLAUR domain-containing protein 6 isoform X1

      UniProtKB/Swiss-Prot
      B3KWC0, Q4G121, Q53TR3, Q659B1, Q86Y78

    3. XM_054340549.1 → XP_054196524.1  ly6/PLAUR domain-containing protein 6 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86Y78.1 GenPept UniProtKB/Swiss-Prot:Q86Y78

    Gene LinkOut

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