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PCDH7 protocadherin 7 [ Homo sapiens (human) ]

Gene ID: 5099, updated on 17-Sep-2024

Summary

Official Symbol
PCDH7provided by HGNC
Official Full Name
protocadherin 7provided by HGNC
Primary source
HGNC:HGNC:8659
See related
Ensembl:ENSG00000169851 MIM:602988; AllianceGenome:HGNC:8659
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
BHPCDH; BH-Pcdh; PPP1R120
Summary
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The gene encodes a protein with an extracellular domain containing 7 cadherin repeats. The gene product is an integral membrane protein that is thought to function in cell-cell recognition and adhesion. Alternative splicing yields isoforms with unique cytoplasmic tails. [provided by RefSeq, Jul 2008]
Expression
Broad expression in brain (RPKM 10.8), spleen (RPKM 5.9) and 17 other tissues See more
Orthologs
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Genomic context

See PCDH7 in Genome Data Viewer
Location:
4p15.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (30720369..31146800)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (30709348..31135781)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (30721991..31148422)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene cathepsin B pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr4:30106274-30106775 Neighboring gene NANOG hESC enhancer GRCh37_chr4:30149486-30150025 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:30151059-30151682 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:30154558-30155155 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_78156 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_78284 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:30444783-30445382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21404 Neighboring gene uncharacterized LOC124900844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:30722800-30723510 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:30758559-30759758 Neighboring gene NANOG hESC enhancer GRCh37_chr4:30838714-30839274 Neighboring gene MT-CYB pseudogene 43 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_78350 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_78356 Neighboring gene NANOG hESC enhancer GRCh37_chr4:31045251-31045820 Neighboring gene long intergenic non-protein coding RNA 2497 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:31235626-31236825 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:31238182-31239381 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:31293032-31293807 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:31462532-31463731 Neighboring gene uncharacterized LOC105374564

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
A genome-wide screen for interactions reveals a new locus on 4p15 modifying the effect of waist-to-hip ratio on total cholesterol.
EBI GWAS Catalog
Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies.
EBI GWAS Catalog
Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
EBI GWAS Catalog
Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults.
EBI GWAS Catalog
Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ97161

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
 
Component Evidence Code Pubs
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
located_in platelet alpha granule membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
protocadherin-7
Names
BH-protocadherin (brain-heart)
brain-heart protocadherin
protein phosphatase 1, regulatory subunit 120

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)

  1. NM_001173523.2NP_001166994.1  protocadherin-7 isoform d precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (d) represents the longest transcript and encodes the longest isoform (d).
    Source sequence(s)
    AC098595, AC107394, AC110766
    UniProtKB/TrEMBL
    A0A087X2C4, A0A8Q3SI70
    Related
    ENSP00000512266.1, ENST00000695919.1
    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  2. NM_002589.4NP_002580.2  protocadherin-7 isoform a precursor

    See identical proteins and their annotated locations for NP_002580.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a) uses an alternate splice pattern in the 3' CDS and 3' UTR, compared to variant d. The resulting isoform (a) has a shorter and distinct C-terminus, compared to isoform d.
    Source sequence(s)
    AC098595
    Consensus CDS
    CCDS33971.1
    UniProtKB/Swiss-Prot
    O60245, O60246, O60247, Q4W5C4
    UniProtKB/TrEMBL
    A0A8Q3SIA5
    Related
    ENSP00000355243.2, ENST00000361762.3
    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  3. NM_032457.4NP_115833.2  protocadherin-7 isoform c precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (c) uses an alternate in-frame splice site in the 3' coding region, compared to variant d. The resulting isoform (c) lacks an internal segment near the C-terminus, compared to isoform d.
    Source sequence(s)
    AC098595, AC107394, AC110766
    Consensus CDS
    CCDS93490.1
    UniProtKB/TrEMBL
    A0A087X2C4, A0A8V8TM73
    Related
    ENSP00000513121.1, ENST00000511884.7
    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin

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

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    30720369..31146800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    30709348..31135781
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_032456.4: Suppressed sequence

    Description
    NM_032456.4: This RefSeq was removed because currently there is support for the transcript but not for the protein.
  2. NR_172626.1: Suppressed sequence

    Description
    NR_172626.1: This RefSeq was removed because currently there is insufficient support for the transcript.