PCDHA3 protocadherin alpha 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCDHA3provided by HGNC
Official Full Name: protocadherin alpha 3provided by HGNC
Primary source: HGNC:HGNC:8669
See related: Ensembl:ENSG00000255408 MIM:606309; AllianceGenome:HGNC:8669
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: PCDH-ALPHA3
Summary: This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]
Orthologs: mouse all
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Genomic context

Location:: 5q31.3

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (140801057..141012347)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (141326390..141537634)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (140180642..140391932)

Chromosome 5 - NC_000005.10 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 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?

Protocadherin alpha 3 inhibits lung squamous cell carcinoma metastasis and epithelial-mesenchymal transition.
Title: Protocadherin alpha 3 inhibits lung squamous cell carcinoma metastasis and epithelial-mesenchymal transition.
Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia.
Title: Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia.
This study suggested that PCDHA3 as a candidate gene for restless legs syndrome.
Title: Exome sequencing in a family with restless legs syndrome.
Observational study of gene-disease association. (HuGE Navigator)
Title: Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence.

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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

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

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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

SHGC-150174 (e-PCR)
- UniSTS:177424

RH122893 (e-PCR)
- UniSTS:135190

D5S1683E (e-PCR)
- UniSTS:151072

RH118816 (e-PCR)
- UniSTS:138797

PCDHA4_1031 (e-PCR)
- UniSTS:277562

RH91795 (e-PCR)
- UniSTS:85819

IB766 (e-PCR)
- UniSTS:42573

bac5366T (e-PCR)
- UniSTS:181623

bac5373T (e-PCR)
- UniSTS:181625

WI-19540 (e-PCR)
- UniSTS:63886

RH15971 (e-PCR)
- UniSTS:21192

D5S658 (e-PCR)
- UniSTS:82129

D5S546 (e-PCR)
- UniSTS:148183

RH65516 (e-PCR)
- UniSTS:66009

PMC311048P1 (e-PCR)
- UniSTS:272867

A004B11 (e-PCR)
- UniSTS:20196

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 homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
involved_in nervous system development	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

General protein information

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Preferred Names: protocadherin alpha-3

Names: KIAA0345-like 11; PCDH-alpha-3

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_050675.1 RefSeqGene

Range

4860..216150

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GenBank, FASTA, Sequence Viewer (Graphics)
NG_000016.2

Range

67071..278218

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_018906.3 → NP_061729.1 protocadherin alpha-3 isoform 1 precursor

See identical proteins and their annotated locations for NP_061729.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).

Source sequence(s)

AC005609, AC010223, AF152311

Consensus CDS

CCDS54915.1

UniProtKB/Swiss-Prot

O75286, Q9Y5H8

UniProtKB/TrEMBL

A1L2Z5

Related

ENSP00000429808.2, ENST00000522353.3

Conserved Domains (3) summary

cd11304
Location:246 → 346

Cadherin_repeat; Cadherin tandem repeat domain

pfam08266
Location:30 → 111

Cadherin_2; Cadherin-like

pfam15974
Location:799 → 942

Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
NM_031497.2 → NP_113685.1 protocadherin alpha-3 isoform 2 precursor

See identical proteins and their annotated locations for NP_113685.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) utilizes the large, first exon then continues into the downstream intron 1 sequence before terminating. This one-exon transcript encodes a shorter isoform (2), compared to isoform 1. This short variant is represented based on data in PMID:10380929.

Source sequence(s)

AC005609, AF152481

UniProtKB/TrEMBL

A1L2Z5

Related

ENSP00000434086.2, ENST00000532566.3

Conserved Domains (2) summary

cd11304
Location:246 → 346

Cadherin_repeat; Cadherin tandem repeat domain

pfam08266
Location:30 → 111

Cadherin_2; Cadherin-like