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    PKD1L2 polycystin 1 like 2 (gene/pseudogene) [ Homo sapiens (human) ]

    Gene ID: 114780, updated on 3-Apr-2024

    Summary

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    Official Symbol
    PKD1L2provided by HGNC
    Official Full Name
    polycystin 1 like 2 (gene/pseudogene)provided by HGNC
    Primary source
    HGNC:HGNC:21715
    See related
    Ensembl:ENSG00000166473 MIM:607894; AllianceGenome:HGNC:21715
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PC1L2
    Summary
    This gene encodes a member of the polycystin protein family. This protein may function as a G-protein-coupled component or regulator of cation channel pores. The long isoform of this protein contains 11 transmembrane domains, a latrophilin/CL-1-like GPCR proteolytic site (GPS) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. Alternative splicing results in multiple transcript variants encoding distinct isoforms. This gene is a polymorphic pseudogene in humans. [provided by RefSeq, May 2022]
    Annotation information
    Annotation category: suggests misassembly
    Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
    Expression
    Biased expression in fat (RPKM 3.7), heart (RPKM 1.2) and 7 other tissues See more
    Orthologs
    all
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    Genomic context

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    See PKD1L2 in Genome Data Viewer
    Location:
    16q23.2
    Exon count:
    43
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (81100875..81220394, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (87162065..87281147, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (81134480..81253999, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371361 Neighboring gene chromosome 16 open reading frame 46 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81110606-81111266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81111267-81111925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7752 Neighboring gene RNA, U6 small nuclear 1191, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81150474-81151032 Neighboring gene glycine cleavage system protein H Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81171151-81171768 Neighboring gene Sharpr-MPRA regulatory region 3111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81191716-81192216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81246022-81246522 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:81255488-81255706 Neighboring gene beta-carotene oxygenase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7755 Neighboring gene gigaxonin Neighboring gene microRNA 4720

    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. A copy number variation in PKD1L2 is associated with colorectal cancer predisposition in korean population. Park C, et al. Int J Cancer, 2017 Jan 1. PMID 27605020
    2. The TRPP subfamily and polycystin-1 proteins. Semmo M, et al. Handb Exp Pharmacol, 2014. PMID 24756726
    3. Upregulation of PKD1L2 provokes a complex neuromuscular disease in the mouse. Mackenzie FE, et al. Hum Mol Genet, 2009 Oct 1. PMID 19578180, Free PMC Article
    4. Polycystin-1L2 is a novel G-protein-binding protein. Yuasa T, et al. Genomics, 2004 Jul. PMID 15203210
    5. Identification of two novel polycystic kidney disease-1-like genes in human and mouse genomes. Li A, et al. Genomics, 2003 Jun. PMID 12782129

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Study found an association between a 6.2 kb dele- tion in the PKD1L2 gene and colorectal cancer in a Korean population.
      Title: A copy number variation in PKD1L2 is associated with colorectal cancer predisposition in korean population.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.
    3. Ectopic expression of PKD1L2 in transgenic mice caused severe muscle atrophy.
      Title: Upregulation of PKD1L2 provokes a complex neuromuscular disease in the mouse.
    4. PKD1L2 is expressed in the developing and adult heart and kidney.
      Title: Polycystin-1L2 is a novel G-protein-binding protein.
    5. 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)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of polycystic kidney disease 1-like 2 (PKD1L2) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ45333, DKFZp686J19100

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in calcium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in detection of mechanical stimulus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    polycystin-1-like protein 2
    Names
    PC1-like 2 protein
    polycystic kidney disease 1-like 2
    polycystin-1L2

    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_033236.2 RefSeqGene

      Range
      5001..124542
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001076780.3 → NP_001070248.2  polycystin-1-like protein 2 isoform c precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks several 3' exons but includes an alternate 3' exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (c) is shorter and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AC092718, AC131888

    2. NM_001278423.2 → NP_001265352.1  polycystin-1-like protein 2 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks several 5' and 3' exons but includes alternate 5' and 3' exons, and it thus differs in both UTRs, uses a downstream in-frame start codon and has an alternate 3' coding region, compared to variant 1. The encoded isoform (e) is shorter and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      BC004562, DA326413
      Consensus CDS
      CCDS61999.1
      UniProtKB/Swiss-Prot
      Q7Z442

    3. NM_001278425.3 → NP_001265354.2  polycystin-1-like protein 2 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4, also known as short form) lacks several 5' exons but includes an alternate 5' exon, and it thus differs in the 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      ABBA01016982, AC092718, KF459692

    4. NM_052892.5 → NP_443124.4  polycystin-1-like protein 2 isoform a precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as long form) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      ABBA01016982, AC092718, AC131888, KF459692

    RNA

    1. NR_126532.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, non-coding), which represents the non-functional allele of this polymorphic pseudogene, has an indel that results in a frameshift to a premature termination codon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC092718, AC131888, AK131378, KF459692
      Related
      ENST00000525539.5

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      81100875..81220394 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791800.1 Reference GRCh38.p14 PATCHES

      Range
      149114..268655 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      87162065..87281147 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_182740.1: Suppressed sequence

      Description
      NM_182740.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z442.5 GenPept UniProtKB/Swiss-Prot:Q7Z442

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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