CDH1 protein expression summary - The Human Protein Atlas

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CDH1

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HUMAN PROTEIN ATLAS SUMMARYⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Proteinⁱ Full gene name according to HGNC.	Cadherin 1
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	CDH1 (CD324, UVO, uvomorulin)
Tissue specificityⁱ ??The RNA specificity category is based on mRNA expression levels in the consensus dataset which is calculated from the RNA expression levels in samples from HPA and GTEX. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Tissue enhanced (parathyroid gland)
Tissue expression clusterⁱ The RNA data was used to cluster genes according to their expression across tissues. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Intestine - Vesicular transport (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Cell type enhanced (Distal enterocytes, Glandular and luminal cells, Pancreatic endocrine cells)
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Intestinal epithelial cells - Unknown function (mainly)
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed blood cell samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Group enriched (plasmacytoid DC, myeloid DC)
Brain specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category Read more	Low human brain regional specificity
Cancer prognostic summary	Prognostic marker in renal cancer (favorable)
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location. Read more	Membrane
Subcellular summaryⁱ Describes the main and potential additional location(s) of the encoded protein according to ICC-IF resukt in the Cell Atlas, as well as potential data regarding cell cycle depency (CCD) for the RNA and/or protein expression.	Located in Golgi apparatus, Plasma membrane, Cell Junctions (Single cell variability)
Protein function (UniProt)ⁱ Useful information about the protein provided by UniProt.	Cadherins are calcium-dependent cell adhesion proteins 1. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. CDH1 is involved in mechanisms regulating cell-cell adhesions, mobility and proliferation of epithelial cells 2. Has a potent invasive suppressor role. It is a ligand for integrin alpha-E/beta-7.... show less
Biological process (UniProt)ⁱ Keywords assigned by UniProt to proteins because they are involved in a particular biological process.	Cell adhesion
Disease involvementⁱ Disease related keywords assigned by UniProt combined with Cancer-related genes and FDA approved drug targets Read more	Cancer-related genes, Disease variant, Ectodermal dysplasia
Ligand (UniProt)ⁱ Keywords assigned by UniProt to proteins because they bind, are associated with, or whose activity is dependent of some molecule.	Calcium, Metal-binding
Gene summary (Entrez)ⁱ Useful information about the gene from Entrez	This gene encodes a classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium-dependent cell-cell adhesion protein is comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Mutations in this gene are correlated with gastric, breast, colorectal, thyroid and ovarian cancer. Loss of function of this gene is thought to contribute to cancer progression by increasing proliferation, invasion, and/or metastasis. The ectodomain of this protein mediates bacterial adhesion to mammalian cells and the cytoplasmic domain is required for internalization. This gene is present in a gene cluster with other members of the cadherin family on chromosome 16. [provided by RefSeq, Nov 2015]... show less

TISSUEⁱ Summary of data presented in the Tissue section, with a representative image of protein expression (left) and an interactive chart showing the tissue-specific mRNA expression (right). The image and the chart are clickable and will redirect to more Tissue data. This section contains information regarding the expression profiles of protein-coding genes in normal human tissue, both on the mRNA and protein level. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry. Read more

Tissue expression clusterⁱ The RNA data was used to cluster genes according to their expression across tissues. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Intestine - Vesicular transport (mainly)
Tissue specificityⁱ The RNA specificity category is based on mRNA expression levels in the consensus dataset which is calculated from the RNA expression levels in samples from HPA and GTEX. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Tissue enhanced (parathyroid gland)
Tissue distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA and GTEX. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many
Protein expressionⁱ A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation. "Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile. Read more	Cytoplasmic and membranous expression in epithelial cells.

BRAINⁱ Summary of data presented in the Brain Atlas and a representative image of mRNA expression in the human brain. The image is clickable and will redirect to more Brain Atlas data. The Brain Atlas explores the protein expression in the mammalian brain by visualization and integration of data from three mammalian species (human, pig and mouse). Transcriptomics data combined with affinity-based protein in situ localization down to single cell level is available in a brain-centric sub atlas of the Human Protein Atlas. Read more

Human regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity
Pig regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity
Mouse regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity

SINGLE CELL TYPEⁱ Summary of data presented in the Single cell Type section, with an interactive chart showing the cell type-specific mRNA expression. The chart is clickable and will redirect to more Cell Type data. This section contains information about single cell type RNA expression based on scRNAseq of human tissues. The data also covers transcriptomics analysis of human blood and cultured cell lines. Read more

Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Intestinal epithelial cells - Unknown function (mainly)
Cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Cell type enhanced (Distal enterocytes, Glandular and luminal cells, Pancreatic endocrine cells)

TISSUE CELL TYPEⁱ

Alveolar cells type 2

Colon enterocytes

Mesothelial cells

Prostate glandular cells

Thyroid glandular cells

Classificationⁱ

Cell type enriched in 6 tissues

PATHOLOGYⁱ Summary of data presented in the Pathology section, with representative images of protein expression in cancer (left) and correlation between mRNA expression and patient survival (right). Images are clickable and redirect to pages with more Pathology data. This section contains mRNA and protein expression data from 17 different forms of human cancer, as well as correlation analysis of mRNA expression and patient survival. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry. Read more
	Renal cancer p<0.001
Prognostic summary	Prognostic marker in renal cancer (favorable)
Cancer specificityⁱ Specificity of RNA expression in 17 cancer types is categorized as either cancer enriched, group enriched, cancer enhanced, low cancer specificity and not detected. Read more	Low cancer specificity
Cancer distributionⁱ Distribution of RNA expression in 17 cancer types is categorized as either detected in single, detected in some, detected in many, detected in all, or not detected. Read more	Detected in all

IMMUNE CELLⁱ Summary of data presented in the Immune Cell section and a representative image of mRNA expression in immune cells in the blood. The image is clickable and will redirect to more immune cell related data. The Immune Cell section contains information regarding single cell type mRNA expression profiles of protein-coding genes in various immune cells in the blood, e.g. B-cells and granulocytes. Read more

Immune cell expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Plasmacytoid DCs - Protein folding (mainly)
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Group enriched (plasmacytoid DC, myeloid DC)

BLOOD PROTEINⁱ Summary of data presented in the Blood proteins section and a representative image of the concentration in plasma and related function for the protein in plasma. The image is clickable and will redirect to more data. The Blood proteins section contains plasma levels of proteins detected in human blood and an analysis of the human secretome (including annotation of the genes predicted to be actively secreted to human blood) is also presented. Read more
Detected in blood by immunoassayⁱ The blood-based immunoassay category applies to actively secreted proteins and is based on plasma or serum protein concentrations established with enzyme-linked immunosorbent assays, compiled from a literature search. The categories include: detected and not detected, where detection refers to a concentration found in the literature search. Read more	No (not applicable)
Detected in blood by mass spectrometryⁱ Detection or not of the gene in blood, based on spectral count estimations from a publicly available mass spectrometry-based plasma proteomics data set obtained from the PeptideAtlas.	Yes
Detected in blood by proximity extension assayⁱ Detection or not of the gene in blood, based on proximity extension assays (Olink) for a longitudinal wellness study covering 76 individuals with three visits during two years. Read more	Yes

SUBCELLULARⁱ Summary of data presented in the Cell Atlas and a representative image of subcellular localization. The Cell Atlas provides RNA expression data derived from RNA sequencing of a large panel of cell lines and protein localization data derived from antibody-based profiling by immunofluorescence confocal microscopy, using a subset of cell lines selected based on RNA expression. Read more

Main locationⁱ Main subcellular location(s) and reliability score(s) for the encoded protein(s) in human cells. The main location(s) may be characterized by presence in all tested cell lines and/or ihigher staining intensity compared to the potential additional location(s). If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively. Read more	Localized to the Plasma membrane, Cell Junctions
Additional locationⁱ Additonal subcellular location(s) for the encoded protein(s) in human cells. The additional location(s) may not be present i all cell lines and may have lower staining intensity compared to the main location(s). If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively. Read more	In addition localized to the Golgi apparatus

CELL LINEⁱ Summary of data presented in the Cell Line section and a representative image of mRNA expression across different human cell lines. The image is clickable and will redirect to more cell line data. This section contains information regarding mRNA expression profiles of human protein-coding genes for a large variety of cell lines. Read more

Cell line expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	BEWO - Transcription regulation (mainly)
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Cell line enhanced (BEWO, CACO-2, CAPAN-2, HaCaT, hTCEpi, MCF7, OE19, RT4, T-47d)
Cell type distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many

METABOLIC

Metabolic info	Not available

GENE INFORMATIONⁱ Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
Gene name	CDH1 (HGNC Symbol)
Synonyms	CD324, UVO, uvomorulin
Description	Cadherin 1 (HGNC Symbol)
Chromosome	16
Cytoband	q22.1
Chromosome location (bp)	68737292 - 68835537
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2
Protein evidence	Evidence at protein level (all genes)
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes CD markers Disease related genes Human disease related genes Plasma proteins
Ensembl	ENSG00000039068 (version 103.38)
Entrez gene	999
UniProt	P12830 (UniProt - Evidence at protein level)
neXtProt	NX_P12830
Antibodypedia	CDH1 antibodies

PROTEIN BROWSERⁱ

CDH1-201

CDH1-202

PROTEIN INFORMATIONⁱ The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database. The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein. The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class. The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Splice variant	UniProt	Protein class	Gene ontology	Length & mass	Signal peptide (predicted)	Transmembrane regions (predicted)
CDH1-201 ENSP00000261769 ENST00000261769	P12830 [Direct mapping] Cadherin-1 E-Cad/CTF1 E-Cad/CTF2 E-Cad/CTF3 A0A0U2ZQU7 [Target identity:100%; Query identity:100%] E-cadherin 1; Epididymis secretory sperm binding protein Show all	CD markers Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Plasma proteins Cancer-related genes Candidate cancer biomarkers Mutated cancer genes Mutational cancer driver genes COSMIC somatic mutations in cancer genes COSMIC Splicing Mutations COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Missense Mutations COSMIC Germline Mutations COSMIC Frameshift Mutations Disease related genes Human disease related genes Cancers Head and neck cancers Cancers of the digestive system Cancers of male genital organs Cancers of endocrine organs Congenital malformations Congenital malformations of skin Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014) Show all	GO:0005509 [calcium ion binding] GO:0005515 [protein binding] GO:0005576 [extracellular region] GO:0005737 [cytoplasm] GO:0005768 [endosome] GO:0005794 [Golgi apparatus] GO:0005802 [trans-Golgi network] GO:0005886 [plasma membrane] GO:0005912 [adherens junction] GO:0007155 [cell adhesion] GO:0007156 [homophilic cell adhesion via plasma membrane adhesion molecules] GO:0007416 [synapse assembly] GO:0008013 [beta-catenin binding] GO:0009636 [response to toxic substance] GO:0009898 [cytoplasmic side of plasma membrane] GO:0010033 [response to organic substance] GO:0010468 [regulation of gene expression] GO:0015629 [actin cytoskeleton] GO:0016020 [membrane] GO:0016021 [integral component of membrane] GO:0016328 [lateral plasma membrane] GO:0016342 [catenin complex] GO:0016600 [flotillin complex] GO:0021983 [pituitary gland development] GO:0022408 [negative regulation of cell-cell adhesion] GO:0030027 [lamellipodium] GO:0030054 [cell junction] GO:0030198 [extracellular matrix organization] GO:0030336 [negative regulation of cell migration] GO:0030506 [ankyrin binding] GO:0030864 [cortical actin cytoskeleton] GO:0031175 [neuron projection development] GO:0032794 [GTPase activating protein binding] GO:0034332 [adherens junction organization] GO:0035635 [entry of bacterium into host cell] GO:0042307 [positive regulation of protein import into nucleus] GO:0042493 [response to drug] GO:0042802 [identical protein binding] GO:0043296 [apical junction complex] GO:0045295 [gamma-catenin binding] GO:0045296 [cadherin binding] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0046872 [metal ion binding] GO:0048471 [perinuclear region of cytoplasm] GO:0050839 [cell adhesion molecule binding] GO:0070062 [extracellular exosome] GO:0071285 [cellular response to lithium ion] GO:0071681 [cellular response to indole-3-methanol] GO:0072659 [protein localization to plasma membrane] GO:0098609 [cell-cell adhesion] GO:0098742 [cell-cell adhesion via plasma-membrane adhesion molecules] GO:0098794 [postsynapse] GO:0098978 [glutamatergic synapse] GO:0099576 [regulation of protein catabolic process at postsynapse, modulating synaptic transmission] Show all	882 aa 97.5 kDa	Yes	1
CDH1-202 ENSP00000414946 ENST00000422392	P12830 [Direct mapping] Cadherin-1 E-Cad/CTF1 E-Cad/CTF2 E-Cad/CTF3 Show all	CD markers Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Plasma proteins Cancer-related genes Candidate cancer biomarkers Mutated cancer genes Mutational cancer driver genes COSMIC somatic mutations in cancer genes COSMIC Splicing Mutations COSMIC Somatic Mutations COSMIC Nonsense Mutations COSMIC Missense Mutations COSMIC Germline Mutations COSMIC Frameshift Mutations Disease related genes Human disease related genes Cancers Head and neck cancers Cancers of the digestive system Cancers of male genital organs Cancers of endocrine organs Congenital malformations Congenital malformations of skin Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Ezkurdia et al 2014) Show all	GO:0005509 [calcium ion binding] GO:0005515 [protein binding] GO:0005576 [extracellular region] GO:0005737 [cytoplasm] GO:0005768 [endosome] GO:0005794 [Golgi apparatus] GO:0005802 [trans-Golgi network] GO:0005886 [plasma membrane] GO:0005912 [adherens junction] GO:0007155 [cell adhesion] GO:0007156 [homophilic cell adhesion via plasma membrane adhesion molecules] GO:0007416 [synapse assembly] GO:0008013 [beta-catenin binding] GO:0009898 [cytoplasmic side of plasma membrane] GO:0010468 [regulation of gene expression] GO:0015629 [actin cytoskeleton] GO:0016020 [membrane] GO:0016021 [integral component of membrane] GO:0016328 [lateral plasma membrane] GO:0016342 [catenin complex] GO:0016600 [flotillin complex] GO:0022408 [negative regulation of cell-cell adhesion] GO:0030027 [lamellipodium] GO:0030054 [cell junction] GO:0030198 [extracellular matrix organization] GO:0030336 [negative regulation of cell migration] GO:0030506 [ankyrin binding] GO:0030864 [cortical actin cytoskeleton] GO:0032794 [GTPase activating protein binding] GO:0034332 [adherens junction organization] GO:0035635 [entry of bacterium into host cell] GO:0042307 [positive regulation of protein import into nucleus] GO:0042802 [identical protein binding] GO:0043296 [apical junction complex] GO:0045295 [gamma-catenin binding] GO:0045296 [cadherin binding] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0046872 [metal ion binding] GO:0048471 [perinuclear region of cytoplasm] GO:0050839 [cell adhesion molecule binding] GO:0070062 [extracellular exosome] GO:0071285 [cellular response to lithium ion] GO:0071681 [cellular response to indole-3-methanol] GO:0072659 [protein localization to plasma membrane] GO:0098609 [cell-cell adhesion] GO:0098742 [cell-cell adhesion via plasma-membrane adhesion molecules] Show all	821 aa 90.9 kDa	Yes	1

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The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.