PCDHA@ protocadherin alpha cluster, complex locus [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCDHA@provided by HGNC
Official Full Name: protocadherin alpha cluster, complex locusprovided by HGNC
Primary source: HGNC:HGNC:8662
See related: MIM:604966; AllianceGenome:HGNC:8662
Gene type: other
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CNR1; CNRS1
Summary: The protocadherin alpha gene cluster is one of three related clusters tandemly linked on chromosome five. The clusters have a genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 genes and 1 pseudogene, which are members of the cadherin superfamily and related to the mouse CNR genes. The sequence of the 13 upstream genes and the pseudogene are highly similar to one another, while a subfamily (C) contains two more distantly related coding sequences. The alpha cluster genes are organized in a tandem array of 15 large, variable region exons followed by a constant region, which contains 3 exons shared by all genes in the cluster. Each variable region exon encodes an extracellular domain comprised of 6 cadherin ectodomains and a transmembrane region. The constant region exons encode a common cytoplasmic tail. These neural adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the alpha cluster genes. [provided by RefSeq, Jul 2008]
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Genomic context

Location:: 5q31.3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (140786136..141012344)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (141311469..141537631)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (140165721..140391929)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Decreased Levels of DNA Methylation in the PCDHA Gene Cluster as a Risk Factor for Early-Onset High Myopia in Young Children.
Title: Decreased Levels of DNA Methylation in the PCDHA Gene Cluster as a Risk Factor for Early-Onset High Myopia in Young Children.
Association between Genetic Variants in DUSP15, CNTNAP2, and PCDHA Genes and Risk of Childhood Autism Spectrum Disorder.
Title: Association between Genetic Variants in DUSP15, CNTNAP2, and PCDHA Genes and Risk of Childhood Autism Spectrum Disorder.
Results provide evidence of PCDHA as a potential candidate gene for autism
Title: Protocadherin α (PCDHA) as a novel susceptibility gene for autism.
PCDHs are candidate tumor suppressors that modulate regulatory pathways critical in development and disease, such as canonical Wnt signaling
Title: Frequent long-range epigenetic silencing of protocadherin gene clusters on chromosome 5q31 in Wilms' tumor.
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.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: A multivariate analysis of 59 candidate genes in personality traits: the temperament and character inventory.

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Phenotypes

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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)

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

PCDHA9_3148 (e-PCR)
- UniSTS:462386

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

PCDHAC1__5835 (e-PCR)
- UniSTS:463779

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

General protein information

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Preferred Names: protocadherin alpha cluster

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.