PCDH12 protocadherin 12 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCDH12provided by HGNC
Official Full Name: protocadherin 12provided by HGNC
Primary source: HGNC:HGNC:8657
See related: Ensembl:ENSG00000113555 MIM:605622; AllianceGenome:HGNC:8657
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: DMJDS1; VECAD2; VE-cadherin-2
Summary: This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing 6 cadherin repeats, a transmembrane domain and a cytoplasmic tail that differs from those of the classical cadherins. The gene localizes to the region on chromosome 5 where the protocadherin gene clusters reside. The exon organization of this transcript is similar to that of the gene cluster transcripts, notably the first large exon, but no significant sequence homology exists. The function of this cellular adhesion protein is undetermined but mouse protocadherin 12 does not bind catenins and appears to have no affect on cell migration or growth. [provided by RefSeq, Jul 2008]
Expression: Broad expression in placenta (RPKM 15.3), lung (RPKM 10.9) and 20 other tissues See more
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 (141943581..141958202, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (142469537..142484801, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (141323146..141337767, complement)

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
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?

Asynchronous presentation and evolution of homozygous PCDH12 variant-induced exudative retinopathy in two siblings.
Title: Asynchronous presentation and evolution of homozygous PCDH12 variant-induced exudative retinopathy in two siblings.
PCDH12 variants are associated with basal ganglia anomalies and exudative vitreoretinopathy.
Title: PCDH12 variants are associated with basal ganglia anomalies and exudative vitreoretinopathy.
The phenotypic spectrum of PCDH12 associated disorders - Five new cases and review of the literature.
Title: The phenotypic spectrum of PCDH12 associated disorders - Five new cases and review of the literature.
Ophthalmic phenotypes associated with biallelic loss-of-function PCDH12 variants.
Title: Ophthalmic phenotypes associated with biallelic loss-of-function PCDH12 variants.
WHSC1 gene variant is associated with dyskinetic cerebral palsy with epilepsy.
Title: A commentary on a case of new PCDH12 gene variants presented as dyskinetic cerebral palsy with epilepsy.
Autosomal-recessive malformation, diencephalic-mesencephalic junction dysplasia syndrome patients have biallelic mutations in PCDH12 and lack of protein expression.
Title: Loss of Protocadherin-12 Leads to Diencephalic-Mesencephalic Junction Dysplasia Syndrome.
Homozygous PCDH12 mutation is associated with cerebellar ataxia, dystonia, retinopathy, and dysmorphism.
Title: Homozygous PCDH12 variants result in phenotype of cerebellar ataxia, dystonia, retinopathy, and dysmorphism.
Genome-wide analysis to determine the genetic cause of a microcephaly syndrome; found that loss of function of PCDH12 leads to recessive congenital microcephaly with profound developmental disability
Title: Loss of function of PCDH12 underlies recessive microcephaly mimicking intrauterine infection.
PCDH12 may play an important role in human placental development, and proteolytic cleavage in response to external factors, such as cytokines and pathological settings, regulates its activity
Title: Protocadherin-12 cleavage is a regulated process mediated by ADAM10 protein: evidence of shedding up-regulation in pre-eclampsia.
A putative association was also found between protocadherin 12 and cortical folding (asymmetry coefficient of gyrification index).
Title: Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

Associated conditions

Description	Tests
Diencephalic-mesencephalic junction dysplasia syndrome 1 MedGen: C4538630 OMIM: 251280 GeneReviews: Not available	Compare labs

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

PCDH12_368 (e-PCR)
- UniSTS:277558

D5S2298E (e-PCR)
- UniSTS:154506

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	IEA Inferred from Electronic Annotation more info
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in glycogen metabolic process	IEA Inferred from Electronic Annotation more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
involved_in labyrinthine layer development	IEA Inferred from Electronic Annotation more info
involved_in neuron recognition	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cell-cell junction	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: protocadherin-12

Names: VE-cad-2; VE-cadherin 2; vascular cadherin-2; vascular endothelial cadherin 2

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_016580.4 → NP_057664.1 protocadherin-12 precursor

See identical proteins and their annotated locations for NP_057664.1

Status: REVIEWED

Source sequence(s)

AC005740, AF231025, AF240635, CA418447

Consensus CDS

CCDS4269.1

UniProtKB/Swiss-Prot

Q6UXB6, Q96KB8, Q9H7Y6, Q9H8E0, Q9NPG4

UniProtKB/TrEMBL

B2RCB8

Related

ENSP00000231484.3, ENST00000231484.4

Conserved Domains (2) summary

cd11304
Location:251 → 348

Cadherin_repeat; Cadherin tandem repeat domain

cl09101
Location:31 → 111

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