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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
Molecular Biology Databases
Research Materials
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