PCDH18 protocadherin 18 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCDH18provided by HGNC
Official Full Name: protocadherin 18provided by HGNC
Primary source: HGNC:HGNC:14268
See related: Ensembl:ENSG00000189184 MIM:608287; AllianceGenome:HGNC:14268
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: PCDH68L
Summary: This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This gene encodes a protein which contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from those of the classical cadherins. Although its specific function is undetermined, the cadherin-related neuronal receptor is thought to play a role in the establishment and function of specific cell-cell connections in the brain. [provided by RefSeq, Jul 2008]
Expression: Broad expression in placenta (RPKM 18.1), endometrium (RPKM 17.7) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q28.3

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (137518918..137532494, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (140842322..140855898, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (138440072..138453648, complement)

Chromosome 4 - NC_000004.12 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
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 results suggested that PCDH18 was a putative tumor suppressor with epigenetic silencing in colorectal cancer and a potential biomarker for colorectal cancer diagnosis.
Title: PCDH18 is frequently inactivated by promoter methylation in colorectal cancer.
A homozygous PCDH18 missense mutation (S1006L)from familial hemophagocytic lymphohistiocytosis type 2 patient destabilized the protein structure.
Title: Search for the potential "second-hit" mechanism underlying the onset of familial hemophagocytic lymphohistiocytosis type 2 by whole-exome sequencing analysis.

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
A genome-wide meta-analysis of association studies of Cloninger's Temperament Scales. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies a region on chromosome 11q14.3 associated with late rectal bleeding following radiation therapy for prostate cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of retinopathy in individuals without diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. 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

PCDH18_1716 (e-PCR)
- UniSTS:277560

PCDH18 (e-PCR)
- UniSTS:503356

RH92584 (e-PCR)
- UniSTS:84291

SHGC-59301 (e-PCR)
- UniSTS:243

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in brain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info

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

General protein information

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Preferred Names: protocadherin-18

Names: protocadherin 68-like protein

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_001300828.2 → NP_001287757.1 protocadherin-18 isoform 2 precursor

See identical proteins and their annotated locations for NP_001287757.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

AB046782, AK292018, BG541979, BQ017212, BX097655, BX647786

Consensus CDS

CCDS75193.1

UniProtKB/TrEMBL

D6RIG4

Related

ENSP00000390688.2, ENST00000412923.6

Conserved Domains (2) summary

cd11304
Location:470 → 572

Cadherin_repeat; Cadherin tandem repeat domain

cl09101
Location:30 → 111

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
NM_019035.5 → NP_061908.1 protocadherin-18 isoform 1 precursor

See identical proteins and their annotated locations for NP_061908.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AB046782, BG541979, BQ017212, BX097655, BX647786

Consensus CDS

CCDS34064.1

UniProtKB/Swiss-Prot

A8K7K3, B7ZKT1, Q52LS2, Q9HCL0

UniProtKB/TrEMBL

D6RIG4

Related

ENSP00000355082.4, ENST00000344876.9

Conserved Domains (2) summary

cd11304
Location:470 → 572

Cadherin_repeat; Cadherin tandem repeat domain

cl09101
Location:30 → 111

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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

137518918..137532494 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017008311.2 → XP_016863800.1 protocadherin-18 isoform X2
XM_006714239.4 → XP_006714302.1 protocadherin-18 isoform X1

See identical proteins and their annotated locations for XP_006714302.1

Conserved Domains (2) summary

cd11304
Location:470 → 572

Cadherin_repeat; Cadherin tandem repeat domain

cl09101
Location:30 → 111

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