PCDHB9 protocadherin beta 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCDHB9provided by HGNC
Official Full Name: protocadherin beta 9provided by HGNC
Primary source: HGNC:HGNC:8694
See related: Ensembl:ENSG00000177839 MIM:606335; AllianceGenome:HGNC:8694
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: PCDH3H; PCDH-BETA9
Summary: This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]
Orthologs: all
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Genomic context

Location:: 5q31.3

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (141187161..141191541)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (141712475..141716855)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (140566735..140571114)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Protocadherin B9 Is Associated with Human Esophageal Squamous Cell Carcinoma Progression.
Title: Protocadherin B9 Is Associated with Human Esophageal Squamous Cell Carcinoma Progression.
A functional analysis showed that PCDHB9 modulated cell migration and adhesion.
Title: Protocadherin B9 promotes resistance to bicalutamide and is associated with the survival of prostate cancer patients.
Protocadherin B9 plays an important role in the progression rather than the pathogenesis of intestinal-type gastric cancers.
Title: Overexpression of PCDHB9 promotes peritoneal metastasis and correlates with poor prognosis in patients with gastric cancer.

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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

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

D8S2279 (e-PCR)
- UniSTS:473907

PCDHB16_1917 (e-PCR)
- UniSTS:280895

D15S1477 (e-PCR)
- UniSTS:474482

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 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	NAS Non-traceable Author Statement more info	PubMed
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in chemical synaptic transmission	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 synapse assembly	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protocadherin beta-9

Names: PCDH-beta-9; protocadherin-3h

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_000017.2

Range

155253..159664

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_019119.5 → NP_061992.3 protocadherin beta-9 precursor

See identical proteins and their annotated locations for NP_061992.3

Status: REVIEWED

Source sequence(s)

AB208959, AC244517, AF217749, BC100672, DA726654

Consensus CDS

CCDS75328.1

UniProtKB/Swiss-Prot

Q2M2U8, Q496X9, Q9NRJ8, Q9Y5E1

UniProtKB/TrEMBL

Q3ZB85

Related

ENSP00000478606.1, ENST00000316105.7

Conserved Domains (4) summary

cd11304
Location:247 → 343

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:372 → 449

CA; Cadherin repeats

pfam08266
Location:32 → 112

Cadherin_2; Cadherin-like

pfam16492
Location:686 → 768

Cadherin_C_2; Cadherin cytoplasmic C-terminal