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    PKD1L3 polycystin 1 like 3, transient receptor potential channel interacting [ Homo sapiens (human) ]

    Gene ID: 342372, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PKD1L3provided by HGNC
    Official Full Name
    polycystin 1 like 3, transient receptor potential channel interactingprovided by HGNC
    Primary source
    HGNC:HGNC:21716
    See related
    Ensembl:ENSG00000277481 MIM:607895; AllianceGenome:HGNC:21716
    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
    This gene encodes a member of the polycystin protein family. The encoded protein contains 11 transmembrane domains, a latrophilin/CL-1-like GPCR proteolytic site (GPS) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. This protein may function as a component of cation channel pores.[provided by RefSeq, Apr 2009]
    Expression
    Ubiquitous expression in gall bladder (RPKM 11.1), spleen (RPKM 10.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PKD1L3 in Genome Data Viewer
    Location:
    16q22.2
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (71929538..72000402, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (77746662..77818469, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (71963441..72034301, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:71879724-71880495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:71884603-71885382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11083 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11084 Neighboring gene ataxin 1 like Neighboring gene zinc finger protein 821 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:71918951-71919451 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:71929209-71929774 Neighboring gene IST1 factor associated with ESCRT-III Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:71971508-71972085 Neighboring gene ribosomal protein L39 pseudogene 31 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:72042438-72042637 Neighboring gene ATP synthase F1 subunit alpha pseudogene 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:72057307-72058506 Neighboring gene dihydroorotate dehydrogenase (quinone)

    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 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. Molecular mechanism of the assembly of an acid-sensing receptor ion channel complex. Yu Y, et al. Nat Commun, 2012. PMID 23212381, Free PMC Article
    2. Genetic tracing of the gustatory neural pathway originating from Pkd1l3-expressing type III taste cells in circumvallate and foliate papillae. Yamamoto K, et al. J Neurochem, 2011 Nov. PMID 21883212, Free PMC Article
    3. A novel PKD2L1 C-terminal domain critical for trimerization and channel function. Zheng W, et al. Sci Rep, 2015 Mar 30. PMID 25820328, Free PMC Article
    4. Identification of two novel polycystic kidney disease-1-like genes in human and mouse genomes. Li A, et al. Genomics, 2003 Jun. PMID 12782129
    5. Interaction between PKD1L3 and PKD2L1 through their transmembrane domains is required for localization of PKD2L1 at taste pores in taste cells of circumvallate and foliate papillae. Ishimaru Y, et al. FASEB J, 2010 Oct. PMID 20538909, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. our study identified C1 as the first PKD2L1 domain essential for both PKD2L1 trimerization and channel function, and suggest that PKD2L1 and PKD2L1/PKD1L3 channels share the PKD2L1 trimerization process.
      Title: A novel PKD2L1 C-terminal domain critical for trimerization and channel function.
    2. functions as a channel-forming subunit in an acid-sensing heteromeric complex formed by PKD1L3 and TRPP3
      Title: Molecular mechanism of the assembly of an acid-sensing receptor ion channel complex.
    3. Among the three gustatory regions innervated by peripheral gustatory neurons in the geniculate ganglion, transgenic Pkd1l3 is expressed in the foliate papillae, not in the fungiform papillae or palate.
      Title: Genetic tracing of the gustatory neural pathway originating from Pkd1l3-expressing type III taste cells in circumvallate and foliate papillae.
    4. 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.
    5. the PKD2L1-PKD1L3 complex is involved in acid sensing in vivo
      Title: Activation of polycystic kidney disease-2-like 1 (PKD2L1)-PKD1L3 complex by acid in mouse taste cells.
    6. genes are mapped to chromosomes and gene structures are characterized; protein structure is predicted and contains strong ion channel signature motifs that suggest their possible function as components of cation channel pores
      Title: Identification of two novel polycystic kidney disease-1-like genes in human and mouse genomes.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study.
    EBI GWAS Catalog

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    contributes_to monoatomic cation channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    contributes_to monoatomic cation transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    NOT enables sour taste receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    contributes_to sour taste receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in calcium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    NOT involved_in cellular response to acidic pH ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cellular response to acidic pH ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    NOT involved_in detection of chemical stimulus involved in sensory perception of sour taste ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in detection of chemical stimulus involved in sensory perception of sour taste ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in detection of mechanical stimulus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in monoatomic cation transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in sensory perception of sour taste IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of cation channel complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    colocalizes_with cell surface ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of receptor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    polycystin-1-like protein 3
    Names
    PC1-like 3 protein
    polycystic kidney disease 1-like 3
    polycystic kidney disease protein 1-like 3
    polycystin-1L3

    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.

    Genomic

    1. NG_032958.1 RefSeqGene

      Range
      4577..75441
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_181536.2 → NP_853514.1  polycystin-1-like protein 3 precursor

      See identical proteins and their annotated locations for NP_853514.1

      Status: VALIDATED

      Source sequence(s)
      AC009127, KF459693
      Consensus CDS
      CCDS73912.1
      UniProtKB/Swiss-Prot
      Q7Z443
      Related
      ENSP00000480090.1, ENST00000620267.2
      Conserved Domains (4) summary
      cd00037
      Location:33 → 138
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
      cd01752
      Location:743 → 859
      PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
      pfam08016
      Location:1446 → 1678
      PKD_channel; Polycystin cation channel
      cl02559
      Location:633 → 672
      GPS; GPCR proteolysis site, GPS, motif

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      71929538..72000402 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024450254.2 → XP_024306022.1  polycystin-1-like protein 3 isoform X1

      Conserved Domains (4) summary
      cd00037
      Location:33 → 137
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
      cd01752
      Location:742 → 858
      PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
      cl02559
      Location:632 → 671
      GPS; GPCR proteolysis site, GPS, motif
      cl27887
      Location:1445 → 1677
      PKD_channel; Polycystin cation channel

    2. XM_024450257.2 → XP_024306025.1  polycystin-1-like protein 3 isoform X4

      Conserved Domains (4) summary
      cd00037
      Location:33 → 138
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
      PLN03223
      Location:1493 → 1645
      PLN03223; Polycystin cation channel protein; Provisional
      cd01752
      Location:681 → 797
      PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
      cl02559
      Location:571 → 610
      GPS; GPCR proteolysis site, GPS, motif

    3. XM_024450256.2 → XP_024306024.1  polycystin-1-like protein 3 isoform X3

      Conserved Domains (4) summary
      cd00037
      Location:33 → 138
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
      cd01752
      Location:684 → 800
      PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
      cl02559
      Location:574 → 613
      GPS; GPCR proteolysis site, GPS, motif
      cl27887
      Location:1387 → 1619
      PKD_channel; Polycystin cation channel

    4. XM_024450255.2 → XP_024306023.1  polycystin-1-like protein 3 isoform X2

      Conserved Domains (4) summary
      cd00037
      Location:33 → 138
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
      cd01752
      Location:743 → 859
      PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
      cl02559
      Location:633 → 672
      GPS; GPCR proteolysis site, GPS, motif
      cl27887
      Location:1440 → 1672
      PKD_channel; Polycystin cation channel

    5. XM_024450260.1 → XP_024306028.1  polycystin-1-like protein 3 isoform X6

      Conserved Domains (3) summary
      cd01752
      Location:507 → 623
      PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
      cl02559
      Location:397 → 436
      GPS; GPCR proteolysis site, GPS, motif
      cl27887
      Location:1210 → 1442
      PKD_channel; Polycystin cation channel

    6. XM_024450258.1 → XP_024306026.1  polycystin-1-like protein 3 isoform X5

      Conserved Domains (3) summary
      cd01752
      Location:559 → 675
      PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
      cl02559
      Location:449 → 488
      GPS; GPCR proteolysis site, GPS, motif
      cl27887
      Location:1262 → 1494
      PKD_channel; Polycystin cation channel

    7. XM_024450259.1 → XP_024306027.1  polycystin-1-like protein 3 isoform X5

      Conserved Domains (3) summary
      cd01752
      Location:559 → 675
      PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
      cl02559
      Location:449 → 488
      GPS; GPCR proteolysis site, GPS, motif
      cl27887
      Location:1262 → 1494
      PKD_channel; Polycystin cation channel

    8. XM_017023201.2 → XP_016878690.1  polycystin-1-like protein 3 isoform X7

    9. XM_017023202.2 → XP_016878691.1  polycystin-1-like protein 3 isoform X8

    10. XM_017023203.2 → XP_016878692.1  polycystin-1-like protein 3 isoform X9

    11. XM_017023204.2 → XP_016878693.1  polycystin-1-like protein 3 isoform X10

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      77746662..77818469 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054380223.1 → XP_054236198.1  polycystin-1-like protein 3 isoform X1

    2. XM_054380226.1 → XP_054236201.1  polycystin-1-like protein 3 isoform X4

    3. XM_054380225.1 → XP_054236200.1  polycystin-1-like protein 3 isoform X3

    4. XM_054380224.1 → XP_054236199.1  polycystin-1-like protein 3 isoform X2

    5. XM_054380229.1 → XP_054236204.1  polycystin-1-like protein 3 isoform X6

    6. XM_054380227.1 → XP_054236202.1  polycystin-1-like protein 3 isoform X5

    7. XM_054380228.1 → XP_054236203.1  polycystin-1-like protein 3 isoform X5

    8. XM_054380232.1 → XP_054236207.1  polycystin-1-like protein 3 isoform X11

    9. XM_054380230.1 → XP_054236205.1  polycystin-1-like protein 3 isoform X7

    10. XM_054380231.1 → XP_054236206.1  polycystin-1-like protein 3 isoform X8

    11. XM_054380233.1 → XP_054236208.1  polycystin-1-like protein 3 isoform X9

    12. XM_054380234.1 → XP_054236209.1  polycystin-1-like protein 3 isoform X10

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z443.1 GenPept UniProtKB/Swiss-Prot:Q7Z443

    Gene LinkOut

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    Chemical Information
    Molecular Biology Databases
    Research Materials