PCDH1 protocadherin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCDH1provided by HGNC
Official Full Name: protocadherin 1provided by HGNC
Primary source: HGNC:HGNC:8655
See related: Ensembl:ENSG00000156453 MIM:603626; AllianceGenome:HGNC:8655
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: PC42; PCDH42
Summary: This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in brain (RPKM 10.0), colon (RPKM 8.9) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q31.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (141853090..141878410, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (142379045..142404656, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (141232655..141257975, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

Insight into the Interplay of Gd-IgA1, HMGB1, RAGE and PCDH1 in IgA Vasculitis (IgAV).
Title: Insight into the Interplay of Gd-IgA1, HMGB1, RAGE and PCDH1 in IgA Vasculitis (IgAV).
PCDH1 promotes progression of pancreatic ductal adenocarcinoma via activation of NF-kappaB signalling by interacting with KPNB1.
Title: PCDH1 promotes progression of pancreatic ductal adenocarcinoma via activation of NF-κB signalling by interacting with KPNB1.
identification of the human asthma-associated gene protocadherin-1 as an essential determinant of entry and infection in pulmonary endothelial cells by two hantaviruses that cause hantavirus pulmonary syndrome, Andes virus and Sin Nombre virus; the surface glycoproteins of ANDV and SNV directly recognize the outermost extracellular repeat domain of PCDH1-a member of the cadherin superfamily--to exploit PCDH1 for entry
Title: Protocadherin-1 is essential for cell entry by New World hantaviruses.
Results show that PCDH1 is localized to the cell membrane of bronchial epithelial cells basolateral to the adherens junction. Its expression is not reduced nor delocalized in asthma even though PCDH1 contributes to homotypic adhesion, epithelial barrier formation and repair.
Title: Protocadherin-1 Localization and Cell-Adhesion Function in Airway Epithelial Cells in Asthma.
PCDH1 is important for airway function as a physical barrier, and its dysfunction is involved in the pathogenesis of allergic airway inflammation.
Title: Protocadherin-1 is a glucocorticoid-responsive critical regulator of airway epithelial barrier function.
PCDH1 and SMAD3 act in a single pathway in asthma susceptibility that affects sensitivity of the airway epithelium to TGF-beta.
Title: Protocadherin-1 binds to SMAD3 and suppresses TGF-β1-induced gene transcription.
Common variations in PCDH1 increase the risk of developing both transient early asthma and atopic dermatitis in early childhood
Title: The PCDH1 gene and asthma in early childhood.
genetic polymorphism is associated with subphenotypes of asthma in German children
Title: Genetic variants in Protocadherin-1, bronchial hyper-responsiveness, and asthma subphenotypes in German children.
PCDH1 gene variant IVS3-116 associates with eczema in two independent birth cohorts in Netherlands.
Title: Protocadherin-1 polymorphisms are associated with eczema in two Dutch birth cohorts.
PCDH1 transcripts display remarkable variability in expression of conserved intracellular signaling domains; enhanced PCDH1 expression levels strongly correlate with differentiation of bronchial epithelial cells.
Title: Characterization of protocadherin-1 expression in primary bronchial epithelial cells: association with epithelial cell differentiation.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide meta-analysis identifies two novel loci associated with high myopia in the Han Chinese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies. 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

PCDH1 (e-PCR)
- UniSTS:479901

WI-7860 (e-PCR)
- UniSTS:42160

5q31-33_43 (e-PCR)
- UniSTS:256509

5q31-33_44 (e-PCR)
- UniSTS:256510

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell signaling	TAS Traceable Author Statement more info	PubMed
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
involved_in nervous system development	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cell junction	IDA Inferred from Direct Assay more info
located_in cell-cell junction	TAS Traceable Author Statement more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: protocadherin-1

Names: cadherin-like 1; cadherin-like protein 1; protocadherin 42

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.

mRNA and Protein(s)

NM_001278613.2 → NP_001265542.1 protocadherin-1 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) has an alternate 5' exon and lacks two 3' exons. Its transcription extends past a splice site that is used in variant 2, resulting in a novel 3' coding region and 3' UTR compared to variant 2. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 2.

Source sequence(s)

AK300564, AK304231, BC035812, HO663512

UniProtKB/TrEMBL

B4E2D8

Related

ENST00000357517.6

Conserved Domains (3) summary

cd11304
Location:528 → 624

Cadherin_repeat; Cadherin tandem repeat domain

pfam08374
Location:831 → 1042

Protocadherin; Protocadherin

cl09101
Location:76 → 154

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
NM_001278615.1 → NP_001265544.1 protocadherin-1 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks two 5' and 3' exons, respectively. It has an alternate 5' exon and its transcription extends past a splice site that is used in variant 2, resulting in a novel 3' coding region and 3' UTR compared to variant 2. It encodes isoform 4 which has a shorter N-terminus and a shorter and distinct C-terminus, compared to isoform 2.

Source sequence(s)

AK308338, BC035812

UniProtKB/TrEMBL

B4DUA8

Related

ENST00000511044.1

Conserved Domains (2) summary

cd11304
Location:133 → 229

Cadherin_repeat; Cadherin tandem repeat domain

pfam08374
Location:436 → 647

Protocadherin; Protocadherin
NM_002587.5 → NP_002578.2 protocadherin-1 isoform 1 precursor

See identical proteins and their annotated locations for NP_002578.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) lacks two exons and its transcription extends past a splice site that is used in variant 2, resulting in a novel 3' coding region and 3' UTR compared to variant 2. It encodes isoform 1 which is shorter and has a distinct C-terminus, compared to isoform 2.

Source sequence(s)

AK289512, AK304231, BC035812

Consensus CDS

CCDS43375.1

UniProtKB/Swiss-Prot

Q08174, Q8IUP2

UniProtKB/TrEMBL

A8K0E7

Related

ENSP00000378043.3, ENST00000394536.4

Conserved Domains (3) summary

cd11304
Location:512 → 608

Cadherin_repeat; Cadherin tandem repeat domain

pfam08374
Location:815 → 1026

Protocadherin; Protocadherin

cl09101
Location:60 → 138

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
NM_032420.5 → NP_115796.2 protocadherin-1 isoform 2 precursor

See identical proteins and their annotated locations for NP_115796.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).

Source sequence(s)

AC094107, AK304231, BC035812, BM680840, DA096772, L11369

Consensus CDS

CCDS4267.1

UniProtKB/TrEMBL

A8K0E7

Related

ENSP00000287008.3, ENST00000287008.8

Conserved Domains (3) summary

cd11304
Location:512 → 608

Cadherin_repeat; Cadherin tandem repeat domain

pfam08374
Location:815 → 1026

Protocadherin; Protocadherin

cl09101
Location:60 → 138

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

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_000005.10 Reference GRCh38.p14 Primary Assembly

Range

141853090..141878410 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005268452.4 → XP_005268509.2 protocadherin-1 isoform X1

UniProtKB/TrEMBL

B3KQM8

Conserved Domains (3) summary

cd11304
Location:528 → 624

Cadherin_repeat; Cadherin tandem repeat domain

pfam08374
Location:831 → 1042

Protocadherin

cl09101
Location:76 → 154

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
XM_005268454.6 → XP_005268511.2 protocadherin-1 isoform X2

UniProtKB/TrEMBL

B4E2D8

Conserved Domains (3) summary

cd11304
Location:528 → 624

Cadherin_repeat; Cadherin tandem repeat domain

pfam08374
Location:831 → 1042

Protocadherin

cl09101
Location:76 → 154

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
XM_017009517.3 → XP_016865006.1 protocadherin-1 isoform X3

UniProtKB/TrEMBL

B3KQM8

Conserved Domains (2) summary

cd11304
Location:133 → 229

Cadherin_repeat; Cadherin tandem repeat domain

pfam08374
Location:436 → 647

Protocadherin; Protocadherin