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

Summary

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

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_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

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

D19S846 (e-PCR)
- UniSTS:154129

RH91143 (e-PCR)
- UniSTS:84009

SHGC-60677 (e-PCR)
- UniSTS:80973

D16S2946 (e-PCR)
- UniSTS:26484

SHGC-60641 (e-PCR)
- UniSTS:56229

NIB727 (e-PCR)
- UniSTS:2812

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 more info	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

NG_032958.1 RefSeqGene

Range

4577..75441

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

71929538..72000402 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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
XM_017023201.2 → XP_016878690.1 polycystin-1-like protein 3 isoform X7
XM_017023202.2 → XP_016878691.1 polycystin-1-like protein 3 isoform X8
XM_017023203.2 → XP_016878692.1 polycystin-1-like protein 3 isoform X9
XM_017023204.2 → XP_016878693.1 polycystin-1-like protein 3 isoform X10