PCDH17 protocadherin 17 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCDH17provided by HGNC
Official Full Name: protocadherin 17provided by HGNC
Primary source: HGNC:HGNC:14267
See related: Ensembl:ENSG00000118946 MIM:611760; AllianceGenome:HGNC:14267
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: PCH68; PCDH68
Summary: This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein contains six extracellular cadherin domains, a transmembrane domain, and a cytoplasmic tail differing from those of the classical cadherins. The encoded protein may 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 spleen (RPKM 10.8), brain (RPKM 7.3) and 14 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 13q21.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (57630108..57729311)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (56846361..56945624)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (58205878..58303445)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ubiquitin ligase NEDD4 promotes the proliferation of hepatocellular carcinoma cells through targeting PCDH17 protein for ubiquitination and degradation.
Title: Ubiquitin ligase NEDD4 promotes the proliferation of hepatocellular carcinoma cells through targeting PCDH17 protein for ubiquitination and degradation.
PCDH17 gene promoter methylation status in a cohort of Egyptian women with epithelial ovarian cancer.
Title: PCDH17 gene promoter methylation status in a cohort of Egyptian women with epithelial ovarian cancer.
Repression of protocadherin 17 is correlated with elevated angiogenesis and hypoxia markers in female patients with breast cancer.
Title: Repression of protocadherin 17 is correlated with elevated angiogenesis and hypoxia markers in female patients with breast cancer.
MiR-23a-3p promoted G1/S cell cycle transition by targeting protocadherin17 in hepatocellular carcinoma.
Title: MiR-23a-3p promoted G1/S cell cycle transition by targeting protocadherin17 in hepatocellular carcinoma.
PCDH17 gene was silenced by DNA methylation in acute myeloid leukemia (AML). Low PCDH17 expression is associated with distinct clinical and biological features and improves risk stratification in patients with AML.
Title: Reduced protocadherin17 expression in leukemia stem cells: the clinical and biological effect in acute myeloid leukemia.
PCDH17 is downregulated in laryngeal squamous cell carcinoma.
Title: MiR-196b affects the progression and prognosis of human LSCC through targeting PCDH-17.
Aberrant hypermethylation in the promoter might be the explanation of PCDH17 downregulated in PCDH17 and promoted the development of nasopharyngeal cancer(NPC).
Title: Aberrant promoter methylation reduced the expression of protocadherin 17 in nasopharyngeal cancer.
Study found elevated promoter methylation and decreased expression of PCDH10 and PCDH17 in advanced gastric lesions, suggesting that elevated PCDH10 and PCDH17 methylation may be an early event in gastric carcinogenesis.
Title: Methylation and Expression of Nonclustered Protocadherins Encoding Genes and Risk of Precancerous Gastric Lesions in a High-Risk Population.
PCDH17 methylation is detectable in serum of cancer patients.
Title: Recurrent transcriptional loss of the PCDH17 tumor suppressor in laryngeal squamous cell carcinoma is partially mediated by aberrant promoter DNA methylation.
We report a genetic association with mood disorders within the genomic region spanning PCDH17. A consistent pattern of allelic association, involving cognition, neuroticism as personality trait, structural and functional imaging, was found in independent samples and in expression of the PCDH17 gene in brain tissues.
Title: The protocadherin 17 gene affects cognition, personality, amygdala structure and function, synapse development and risk of major mood disorders.

Submit: New GeneRIF Correction See all GeneRIFs (27)

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

PCDH17_1260 (e-PCR)
- UniSTS:277559

SHGC-56621 (e-PCR)
- UniSTS:30026

G20769 (e-PCR)
- UniSTS:57939

A006F33 (e-PCR)
- UniSTS:57940

SHGC-33151 (e-PCR)
- UniSTS:68196

RH44773 (e-PCR)
- UniSTS:76241

WI-18283 (e-PCR)
- UniSTS:6377

PCDH17 (e-PCR)
- UniSTS:505330

LOC144997 (e-PCR)
- UniSTS:505331

SHGC-30612 (e-PCR)
- UniSTS:13816

D13S1303 (e-PCR), detects polymorphism
- UniSTS:49918

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 adult behavior	IEA Inferred from Electronic Annotation 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
involved_in negative regulation of synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in presynaptic active zone assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic vesicle clustering	IEA Inferred from Electronic Annotation more info
involved_in synaptic membrane adhesion	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in GABA-ergic synapse	IEA Inferred from Electronic Annotation more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
located_in presynaptic membrane	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: protocadherin-17

Names: protocadherin 68

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001040429.3 → NP_001035519.1 protocadherin-17 precursor

See identical proteins and their annotated locations for NP_001035519.1

Status: REVIEWED

Source sequence(s)

AL445216, AL445288, BC028165

Consensus CDS

CCDS31986.1

UniProtKB/Swiss-Prot

A8K1R5, O14917, Q5VVW9, Q5VVX0

Related

ENSP00000367151.3, ENST00000377918.8

Conserved Domains (2) summary

cd11304
Location:247 → 347

Cadherin_repeat; Cadherin tandem repeat domain

cl09101
Location:21 → 112

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_000013.11 Reference GRCh38.p14 Primary Assembly

Range

57630108..57729311

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005266357.3 → XP_005266414.1 protocadherin-17 isoform X1

See identical proteins and their annotated locations for XP_005266414.1

UniProtKB/Swiss-Prot

A8K1R5, O14917, Q5VVW9, Q5VVX0

Conserved Domains (2) summary

cd11304
Location:247 → 347

Cadherin_repeat; Cadherin tandem repeat domain

cl09101
Location:21 → 112

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
XM_047430276.1 → XP_047286232.1 protocadherin-17 isoform X2
XM_017020547.2 → XP_016876036.1 protocadherin-17 isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060937.1 Alternate T2T-CHM13v2.0

Range

56846361..56945624

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054374466.1 → XP_054230441.1 protocadherin-17 isoform X1

UniProtKB/Swiss-Prot

A8K1R5, O14917, Q5VVW9, Q5VVX0
XM_054374467.1 → XP_054230442.1 protocadherin-17 isoform X2
XM_054374468.1 → XP_054230443.1 protocadherin-17 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_014459.2: Suppressed sequence

Description

NM_014459.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.