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

Gene ID: 342372, updated on 5-Jan-2025

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: 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. The response of PKD1L3/PKD2L1 to acid stimuli is inhibited by capsaicin and its pungent analogs. Ishii S, et al. FEBS J, 2012 May. PMID 22420714, 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. 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
  5. Acetic acid activates PKD1L3-PKD2L1 channel--a candidate sour taste receptor. Ishii S, et al. Biochem Biophys Res Commun, 2009 Jul 31. PMID 19464260

See all (17) 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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)

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 calcium-activated cation channel activity ISS
Inferred from Sequence or Structural Similarity
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 pH-gated monoatomic ion channel activity IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
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 transmembrane transport IDA
Inferred from Direct Assay
more info
 PubMed 
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

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Chemical Information
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