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

Gene ID: 114780, updated on 23-Nov-2021

Summary

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
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. 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. This gene appears to be a polymorphic pseudogene in humans, and the reference genome encodes a non-functional allele. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2019]
Annotation information
Annotation category: suggests misassembly
Expression
Biased expression in fat (RPKM 3.7), heart (RPKM 1.2) and 7 other tissues See more
Orthologs
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Genomic context

See PKD1L2 in Genome Data Viewer
Location:
16q23.2
Exon count:
44
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (81100875..81220394, complement)
105.20201022 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 RNA, U6 small nuclear 1191, pseudogene Neighboring gene glycine cleavage system protein H Neighboring gene Sharpr-MPRA regulatory region 3111 Neighboring gene beta-carotene oxygenase 1 Neighboring gene gigaxonin Neighboring gene microRNA 4720

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study.
GeneReviews: Not available

HIV-1 interactions

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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
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
PubMed 
Component Evidence Code Pubs
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
polycystic kidney disease protein 1-like 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_033236.1 RefSeqGene

    Range
    4977..124497
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001076780.2NP_001070248.1  polycystic kidney disease protein 1-like 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)
    AC131888, AY164483, AY371495, BC004562
    UniProtKB/Swiss-Prot
    Q7Z442
    Related
    ENSP00000337397.4, ENST00000337114.8
    Conserved Domains (3) summary
    smart00034
    Location:28153
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam02010
    Location:590901
    REJ; REJ domain
    pfam02140
    Location:170251
    Gal_Lectin; Galactose binding lectin domain
  2. NM_001278423.2NP_001265352.1  polycystic kidney disease protein 1-like 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
    Related
    ENSP00000436309.1, ENST00000531391.5
  3. NM_001278425.2NP_001265354.1  polycystic kidney disease protein 1-like 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)
    AC092718, AY164483, AY371495
    UniProtKB/Swiss-Prot
    Q7Z442
    Related
    ENSP00000434644.1, ENST00000533478.5
    Conserved Domains (3) summary
    smart00303
    Location:595634
    GPS; G-protein-coupled receptor proteolytic site domain
    cd01752
    Location:705824
    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:13021715
    PKD_channel; Polycystin cation channel
  4. NM_052892.4NP_443124.3  polycystic kidney disease protein 1-like 2 isoform a precursor

    See identical proteins and their annotated locations for NP_443124.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also known as long form) represents the functional allele that is absent from the reference genome but present in some human individuals. This variant is the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC092718, AC131888, AK131378, AY164483, AY371495, DB306292
    UniProtKB/Swiss-Prot
    Q7Z442
    Conserved Domains (5) summary
    smart00303
    Location:12801319
    GPS; G-protein-coupled receptor proteolytic site domain
    smart00034
    Location:28153
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    cd01752
    Location:13901509
    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 ...
    pfam02140
    Location:170251
    Gal_Lectin; Galactose binding lectin domain
    cl27887
    Location:19872400
    PKD_channel; Polycystin cation channel

RNA

  1. NR_126532.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, non-coding) represents the non-functional allele found in the reference genome. This variant lacks a single nucleotide that would result in a frameshift due 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, AY164483, AY371495, DB306292
    Related
    ENST00000525539.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    81100875..81220394 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.
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