CDH6 cadherin 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CDH6provided by HGNC
Official Full Name: cadherin 6provided by HGNC
Primary source: HGNC:HGNC:1765
See related: Ensembl:ENSG00000113361 MIM:603007; AllianceGenome:HGNC:1765
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: CAD6; KCAD
Summary: This gene encodes a member of the cadherin superfamily. Cadherins are membrane glycoproteins that mediate homophilic cell-cell adhesion and play critical roles in cell differentiation and morphogenesis. The encoded protein is a type II cadherin and may play a role in kidney development as well as endometrium and placenta formation. Decreased expression of this gene may be associated with tumor growth and metastasis. [provided by RefSeq, May 2011]
Expression: Broad expression in kidney (RPKM 6.1), gall bladder (RPKM 4.1) and 17 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5p13.3

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (31193686..31329146)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (31307253..31442732)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (31193793..31329253)

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?

The GLI2/CDH6 axis enhances migration, invasion and mitochondrial fission of stomach adenocarcinoma cells.
Title: The GLI2/CDH6 axis enhances migration, invasion and mitochondrial fission of stomach adenocarcinoma cells.
Characterization of the role for cadherin 6 in the regulation of human endometrial receptivity.
Title: Characterization of the role for cadherin 6 in the regulation of human endometrial receptivity.
CDH6 and HAGH protein levels in plasma associate with Alzheimer's disease in APOE epsilon4 carriers.
Title: CDH6 and HAGH protein levels in plasma associate with Alzheimer's disease in APOE ε4 carriers.
The low endometrial expression of beta-catenin, E-cadherin and K-cadherin were associated to fertility-related problems, such as primary intertility and recurrent pregnancy loss.
Title: Low endometrial beta-catenin and cadherins expression patterns are predictive for primary infertility and recurrent pregnancy loss.
our findings demonstrate that CDH6 exerts as an important independent biomarker that could predict human osteosarcoma clinical outcomes. miR-223-3p can inhibit cell invasion, migration, growth, and proliferation in osteosarcoma by directly targeting CDH6
Title: miR-223-3p Inhibits Human Osteosarcoma Metastasis and Progression by Directly Targeting CDH6.
Tumor suppressor genes deleted in liver cancer 1 (DLC1), F-box/WD-repeat-containing protein 7 (FBXW7), and cadherin-6 (CDH6) were identified as presumed targets in Cholangiocarcinoma (CC).Inverse correlation between promoter methylation and expression suggested miR-129-2 and members of the miR-200 family (miR-200a, miR-200b, and miR-429) as novel tumor suppressors and oncomiRs, respectively, in CC
Title: Cadherin-6 is a putative tumor suppressor and target of epigenetically dysregulated miR-429 in cholangiocarcinoma.
Data indicate that BRAFV600E, P-cadherin and cadherin 6 protein expressions were correlated with one another.
Title: Concomitant high expression of BRAFV600E, P-cadherin and cadherin 6 is associated with High TNM stage and lymph node metastasis in conventional papillary thyroid carcinoma.
CDH6 is under the control of the transcription factor RUNX2, which we previously described as a crucial mediator of the Id1 pro-invasive function in thyroid tumor cells.
Title: Cadherin 6 is a new RUNX2 target in TGF-β signalling pathway.
The chromatin modifications were determined at five PRC2 targets commonly underexpressed in multiple myeloma (CIITA, CXCL12, GATA2, CDH6 and ICSBP/IRF8). The selected genes were confirmed to be underexpressed in MM compared to normal plasma cells.
Title: Polycomb target genes are silenced in multiple myeloma.

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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

EBI GWAS Catalog

Description
Genome-wide association study identifies BICD1 as a susceptibility gene for emphysema. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

SHGC-11631 (e-PCR)
- UniSTS:31532

D5S599 (e-PCR)
- UniSTS:45361

CDH6_424 (e-PCR)
- UniSTS:277089

D5S108 (e-PCR)
- UniSTS:146802

RH98465 (e-PCR)
- UniSTS:88210

RH48923 (e-PCR)
- UniSTS:52140

PMC311006P2 (e-PCR)
- UniSTS:272829

SGC35576 (e-PCR)
- UniSTS:66772

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables beta-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cadherin binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in Notch signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in adherens junction organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell adhesion	TAS Traceable Author Statement more info	PubMed
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell adhesion mediated by cadherin	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell junction assembly	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
involved_in multicellular organism development	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic membrane adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic membrane adhesion	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
part_of catenin complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cell junction	IDA Inferred from Direct Assay more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay 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

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Preferred Names: cadherin-6

Names: cadherin 6, type 2, K-cadherin (fetal kidney)

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_001362435.2 → NP_001349364.1 cadherin-6 isoform 2 preproprotein

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' CDS and 3' UTR, compared to variant 1, and encodes a protein (isoform 2) with a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AC091898, AC113386

UniProtKB/TrEMBL

D6RF86

Related

ENSP00000424843.1, ENST00000514738.5

Conserved Domains (2) summary

cd11304
Location:163 → 264

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:79 → 157

CA; Cadherin repeats
NM_004932.4 → NP_004923.1 cadherin-6 isoform 1 preproprotein

See identical proteins and their annotated locations for NP_004923.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC091898, D31784, DC353791

Consensus CDS

CCDS3894.1

UniProtKB/Swiss-Prot

A8K5H5, P55285, Q9BWS0

Related

ENSP00000265071.2, ENST00000265071.3

Conserved Domains (3) summary

cd11304
Location:163 → 264

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:79 → 157

CA; Cadherin repeats

pfam01049
Location:645 → 782

Cadherin_C; Cadherin cytoplasmic region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

31193686..31329146

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011513921.4 → XP_011512223.1 cadherin-6 isoform X1

See identical proteins and their annotated locations for XP_011512223.1

UniProtKB/Swiss-Prot

A8K5H5, P55285, Q9BWS0

Conserved Domains (3) summary

cd11304
Location:163 → 264

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:79 → 157

CA; Cadherin repeats

pfam01049
Location:645 → 782

Cadherin_C; Cadherin cytoplasmic region
XM_047416591.1 → XP_047272547.1 cadherin-6 isoform X2