CDH10 cadherin 10 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CDH10provided by HGNC
Official Full Name: cadherin 10provided by HGNC
Primary source: HGNC:HGNC:1749
See related: Ensembl:ENSG00000040731 MIM:604555; AllianceGenome:HGNC:1749
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
Summary: This gene encodes a type II classical cadherin of the cadherin superfamily. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature cadherin protein. These integral membrane proteins mediate calcium-dependent cell-cell adhesion and are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. The extracellular domain consists of 5 subdomains, each containing a cadherin motif, and appears to determine the specificity of the protein's homophilic cell adhesion activity. Type II (atypical) cadherins are defined based on their lack of a histidine-alanine-valine (HAV) cell adhesion recognition sequence specific to type I cadherins. This particular cadherin is predominantly expressed in brain and is putatively involved in synaptic adhesions, axon outgrowth and guidance. Mutations in this gene may be associated with lung squamous cell carcinoma and colorectal cancer in human patients. [provided by RefSeq, Nov 2015]
Expression: Biased expression in brain (RPKM 13.5) and prostate (RPKM 2.1) See more
Orthologs: mouse all
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Genomic context

Location:: 5p14.2-p14.1

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (24487100..24644978, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (24591295..24750171, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (24487209..24645087, complement)

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 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?

G9a-mediated repression of CDH10 in hypoxia enhances breast tumour cell motility and associates with poor survival outcome.
Title: G9a-mediated repression of CDH10 in hypoxia enhances breast tumour cell motility and associates with poor survival outcome.
Loss of CDH10 gene is associated with pancreatic ductal adenocarcinomas.
Title: Alterations of type II classical cadherin, cadherin-10 (CDH10), is associated with pancreatic ductal adenocarcinomas.
Unconventional CDH10, CDH24 and DCHS2 genes harbored frameshift mutations.
Title: Frameshift mutations of cadherin genes DCHS2, CDH10 and CDH24 genes in gastric and colorectal cancers with high microsatellite instability.
The CC genotype of rs4307059 located in the region between CDH9 and CDH10 is associated with completed suicide in a Polish cohort
Title: Analysis of four genes involved in the neurodevelopment shows association of rs4307059 polymorphism in the cadherin 9/10 region with completed suicide.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Common genetic variants on 5p14.1 associate with autism spectrum disorders.

Submit: New GeneRIF Correction

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
Common genetic variants on 5p14.1 associate with autism spectrum disorders. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic determinants of plasma &#x003b2;&#x02082;-glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study in obsessive-compulsive disorder: results from the OCGAS. 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

RH12465 (e-PCR)
- UniSTS:82232

SHGC-153792 (e-PCR)
- UniSTS:184122

HSC1GA082 (e-PCR)
- UniSTS:47437

CDH10_5 (e-PCR)
- UniSTS:277083

G65564 (e-PCR)
- UniSTS:225406

RH79643 (e-PCR)
- UniSTS:87685

RH118910 (e-PCR)
- UniSTS:138902

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
enables calcium ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
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 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	NAS Non-traceable Author Statement more info	PubMed
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 synaptic membrane adhesion	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in GABA-ergic synapse	IEA Inferred from Electronic Annotation more info
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 glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic specialization membrane	IEA Inferred from Electronic Annotation more info
located_in presynaptic active zone membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: cadherin-10

Names: T2-cadherin; cadherin 10 type 2

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_001317222.2 → NP_001304151.1 cadherin-10 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and uses a downstream translation start site compared to variant 1. The encoded isoform (2) has a shorter N-terminus and lacks a predicted signal peptide compared to isoform 1.

Source sequence(s)

BC144168, BM669374, DA316487, DA531048

Conserved Domains (1) summary

pfam01049
Location:41 → 188

Cadherin_C; Cadherin cytoplasmic region
NM_001317224.2 → NP_001304153.1 cadherin-10 isoform 3 preproprotein

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The encoded isoform (3, also known as CDH10_B) is shorter than isoform 1. This isoform (3) may undergo proteolytic processing similar to isoform 1.

Source sequence(s)

AC010387, AC091885

UniProtKB/TrEMBL

X5DNG6

Conserved Domains (3) summary

cd11304
Location:164 → 265

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:80 → 158

CA; Cadherin repeats

pfam01049
Location:633 → 780

Cadherin_C; Cadherin cytoplasmic region
NM_001362460.1 → NP_001349389.1 cadherin-10 isoform 4 preproprotein

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks two in-frame exons in the 3' coding region compared to variant 1. The encoded isoform (4) is shorter than isoform 1. This isoform (4) may undergo proteolytic processing similar to isoform 1.

Source sequence(s)

AC010387, AC091885

UniProtKB/TrEMBL

D6RJG0

Related

ENSP00000425653.1, ENST00000510477.5

Conserved Domains (2) summary

cd11304
Location:164 → 265

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:80 → 158

CA; Cadherin repeats
NM_006727.5 → NP_006718.2 cadherin-10 isoform 1 preproprotein

See identical proteins and their annotated locations for NP_006718.2

Status: REVIEWED

Description

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

Source sequence(s)

AB035303, BM669374, DA316487, DA531048

Consensus CDS

CCDS3892.1

UniProtKB/Swiss-Prot

Q9ULB3, Q9Y6N8

UniProtKB/TrEMBL

X5D8X5

Related

ENSP00000264463.4, ENST00000264463.8

Conserved Domains (3) summary

cd11304
Location:164 → 265

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:80 → 158

CA; Cadherin repeats

pfam01049
Location:635 → 782

Cadherin_C; Cadherin cytoplasmic region

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

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

24487100..24644978 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011513923.3 → XP_011512225.1 cadherin-10 isoform X1

See identical proteins and their annotated locations for XP_011512225.1

UniProtKB/Swiss-Prot

Q9ULB3, Q9Y6N8

UniProtKB/TrEMBL

X5D8X5

Conserved Domains (3) summary

cd11304
Location:164 → 265

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:80 → 158

CA; Cadherin repeats

pfam01049
Location:635 → 782

Cadherin_C; Cadherin cytoplasmic region

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

24591295..24750171 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054351383.1 → XP_054207358.1 cadherin-10 isoform X1

UniProtKB/Swiss-Prot

Q9ULB3, Q9Y6N8

UniProtKB/TrEMBL

X5D8X5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001190450.1: Suppressed sequence

Description

NM_001190450.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.