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

Gene ID: 130574, updated on 5-Mar-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
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Genomic context

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Location:
2q23.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (149329985..149486378)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (149780390..149936801)
105.20220307 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: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 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)

Genotypes

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_2023_10

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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