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CDH4 cadherin 4 [ Homo sapiens (human) ]

Gene ID: 1002, updated on 5-Sep-2021

Summary

Official Symbol
CDH4provided by HGNC
Official Full Name
cadherin 4provided by HGNC
Primary source
HGNC:HGNC:1763
See related
Ensembl:ENSG00000179242 MIM:603006
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
CAD4; RCAD; R-CAD
Summary
This gene is a classical cadherin from the cadherin superfamily. The encoded protein is a calcium-dependent cell-cell adhesion glycoprotein comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Based on studies in chicken and mouse, this cadherin is thought to play an important role during brain segmentation and neuronal outgrowth. In addition, a role in kidney and muscle development is indicated. Of particular interest are studies showing stable cis-heterodimers of cadherins 2 and 4 in cotransfected cell lines. Previously thought to interact in an exclusively homophilic manner, this is the first evidence of cadherin heterodimerization. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
Expression
Biased expression in spleen (RPKM 3.2), brain (RPKM 3.1) and 6 other tissues See more
Orthologs
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Genomic context

See CDH4 in Genome Data Viewer
Location:
20q13.33
Exon count:
18
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (61252261..61940617)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (59827317..60515673)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1718 Neighboring gene uncharacterized LOC105372701 Neighboring gene uncharacterized LOC105372703 Neighboring gene uncharacterized LOC100128310 Neighboring gene Sharpr-MPRA regulatory region 10002 Neighboring gene uncharacterized LOC105372704 Neighboring gene microRNA 1257 Neighboring gene TATA-box binding protein associated factor 4

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study.
GeneReviews: Not available
Genetic determinants of plasma β₂-glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain.
GeneReviews: Not available
Genome-wide association reveals genetic effects on human Aβ42 and τ protein levels in cerebrospinal fluids: a case control study.
GeneReviews: Not available
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
GeneReviews: Not available
Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2.
GeneReviews: Not available
Genome-wide meta-analysis identifies new susceptibility loci for migraine.
GeneReviews: Not available
GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease.
GeneReviews: Not available
Joint influence of small-effect genetic variants on human longevity.
GeneReviews: Not available
Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
GeneReviews: Not available
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ22202, FLJ40547, MGC126700, MGC138355

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cadherin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
part_of catenin complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in integral component of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
cadherin-4
Names
R-cadherin
cadherin 4, type 1, R-cadherin (retinal)
cadherin 4, type 1, preproprotein
retinal cadherin

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_001252338.2NP_001239267.1  cadherin-4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate exon in place of the first two exons compared to variant 1, and the alternate exon has an in-frame translation start site. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AA213385, AK308345, AL109911, AL162457, KF511320
    Conserved Domains (4) summary
    cd11304
    Location:244351
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam01049
    Location:732874
    Cadherin_C; Cadherin cytoplasmic region
    cl07391
    Location:2082
    Cadherin_pro; Cadherin prodomain like
    cl09101
    Location:136236
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  2. NM_001252339.3NP_001239268.1  cadherin-4 isoform 3

    See identical proteins and their annotated locations for NP_001239268.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate exon in place of the first two exons compared to variant 1, but the alternate exon does not have an in-frame translation start site. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AA213385, AK124724, AL109911, AL162457, DC330816, KF511320
    Consensus CDS
    CCDS58784.1
    UniProtKB/Swiss-Prot
    P55283
    Related
    ENSP00000443301.1, ENST00000543233.2
    Conserved Domains (4) summary
    cd11304
    Location:207314
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam01049
    Location:695837
    Cadherin_C; Cadherin cytoplasmic region
    cl07391
    Location:245
    Cadherin_pro; Cadherin prodomain like
    cl09101
    Location:99199
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  3. NM_001794.5NP_001785.2  cadherin-4 isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_001785.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA213385, AL109911, AL365229, BC101651, KF511320
    Consensus CDS
    CCDS13488.1
    UniProtKB/Swiss-Prot
    P55283
    Related
    ENSP00000484928.1, ENST00000614565.5
    Conserved Domains (4) summary
    cd11304
    Location:281388
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam01049
    Location:769911
    Cadherin_C; Cadherin cytoplasmic region
    pfam08758
    Location:30119
    Cadherin_pro; Cadherin prodomain like
    cl09101
    Location:173273
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    61252261..61940617
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_187623.1 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    8603..54269
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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