CDH16 cadherin 16 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CDH16provided by HGNC
Official Full Name: cadherin 16provided by HGNC
Primary source: HGNC:HGNC:1755
See related: Ensembl:ENSG00000166589 MIM:603118; AllianceGenome:HGNC:1755
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 is a member of the cadherin superfamily, genes encoding calcium-dependent, membrane-associated glycoproteins. Mapped to a previously identified cluster of cadherin genes on chromosome 16q22.1, the gene localizes with superfamily members CDH1, CDH3, CDH5, CDH8 and CDH11. The protein consists of an extracellular domain containing 6 cadherin domains, a transmembrane region and a truncated cytoplasmic domain but lacks the prosequence and tripeptide HAV adhesion recognition sequence typical of most classical cadherins. Expression is exclusively in kidney, where the protein functions as the principal mediator of homotypic cellular recognition, playing a role in the morphogenic direction of tissue development. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Mar 2011]
Expression: Restricted expression toward kidney (RPKM 177.1) See more
Orthologs: mouse all
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Genomic context

Location:: 16q22.1

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (66908122..66918885, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (72702422..72713185, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (66942025..66952788, complement)

Chromosome 16 - NC_000016.10 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?

Loss of CDH16 expression is a strong independent predictor for lymph node metastasis in Middle Eastern papillary thyroid cancer.
Title: Loss of CDH16 expression is a strong independent predictor for lymph node metastasis in Middle Eastern papillary thyroid cancer.
Reduced CDH16 expression is linked to poor prognosis in clear cell renal cell carcinoma 16.
Title: Reduced CDH16 expression is linked to poor prognosis in clear cell renal cell carcinoma 16.
Our study expands the clinical and allelic spectrum of known Retinal dystrophies genes, and reveals AGBL5, CDH16, and DNAJC17 as novel disease candidates.
Title: Expanding the clinical, allelic, and locus heterogeneity of retinal dystrophies.
In thyroid carcinomas, as determined by quantitative RT-PCR, CDH16 expression decreases in papillary, follicular, and anaplastic thyroid carcinomas, and the decrease is more pronounced than that of CDH1.
Title: CDH16/Ksp-cadherin is expressed in the developing thyroid gland and is strongly down-regulated in thyroid carcinomas.
The interaction of Ksp-cadherin with alpha B-crystallin is important for the connection of Ksp-cadherin to the cytoskeleton and thus for maintaining tissue integrity in the kidney.
Title: alpha B-crystallin is a cytoplasmic interaction partner of the kidney-specific cadherin-16.
Ksp-cad is a useful tumor type associated marker for distinguishing chromophobe renal cell carcinoma and renal oncocytoma from the wide range of nonintercalated cell-related adult renal epithelial neoplasms.
Title: Expression analysis of kidney-specific cadherin in a wide spectrum of traditional and newly recognized renal epithelial neoplasms: diagnostic and histogenetic implications.
These results indicated that LIF induced multi-lineage differentiation of adult stem-like cells in kidney via cadherin 16.
Title: Leukemia inhibitory factor induces multi-lineage differentiation of adult stem-like cells in kidney via kidney-specific cadherin 16.
Ksp-cadherin expression downregulated inrenal cell carcinoma; this cell adhesion molecule may have role in tumour suppression
Title: Expression of Ksp-cadherin during kidney development and in renal cell carcinoma.

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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

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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	IEA Inferred from Electronic Annotation more info
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
located_in basolateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: cadherin-16

Names: KSP-cadherin; cadherin 16, KSP-cadherin; kidney-specific 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)

NM_001204744.2 → NP_001191673.1 cadherin-16 isoform 2 precursor

See identical proteins and their annotated locations for NP_001191673.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame segment in the 3' coding region, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1.

Source sequence(s)

AY358911, BC027912

Consensus CDS

CCDS56002.1

UniProtKB/TrEMBL

B2R7S8

Related

ENSP00000377619.3, ENST00000394055.7

Conserved Domains (2) summary

cd11304
Location:342 → 445

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:47 → 124

CA; Cadherin repeats
NM_001204745.2 → NP_001191674.1 cadherin-16 isoform 3 precursor

See identical proteins and their annotated locations for NP_001191674.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an in-frame segment in the 3' coding region, as compared to variant 1. The resulting isoform (3) lacks an internal segment, as compared to isoform 1.

Source sequence(s)

AK298255, BC027912, DC361453

Consensus CDS

CCDS58471.1

UniProtKB/TrEMBL

B2R7S8

Related

ENSP00000454784.1, ENST00000565796.5

Conserved Domains (2) summary

cd11304
Location:342 → 445

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:47 → 124

CA; Cadherin repeats
NM_001204746.2 → NP_001191675.1 cadherin-16 isoform 4 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an in-frame segment in the 5' coding region, as compared to variant 1. The resulting isoform (4) lacks an internal segment, as compared to isoform 1.

Source sequence(s)

AK225544, DC361453

Consensus CDS

CCDS58472.1

UniProtKB/TrEMBL

B2R7S8

Related

ENSP00000455263.1, ENST00000568632.5

Conserved Domains (2) summary

cd11304
Location:245 → 348

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:47 → 123

CA; Cadherin repeats
NM_004062.4 → NP_004053.1 cadherin-16 isoform 1 precursor

See identical proteins and their annotated locations for NP_004053.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AF016272, BC027912, DC361453

Consensus CDS

CCDS10823.1

UniProtKB/Swiss-Prot

B4DPA8, H3BPD3, O75309, Q6UW93

UniProtKB/TrEMBL

B2R7S8

Related

ENSP00000299752.4, ENST00000299752.9

Conserved Domains (2) summary

cd11304
Location:342 → 445

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:47 → 124

CA; Cadherin repeats

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_000016.10 Reference GRCh38.p14 Primary Assembly

Range

66908122..66918885 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047433490.1 → XP_047289446.1 cadherin-16 isoform X2
XM_011522807.2 → XP_011521109.1 cadherin-16 isoform X1

UniProtKB/TrEMBL

B2R7S8

Conserved Domains (2) summary

cd11304
Location:342 → 445

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:47 → 124

CA; Cadherin repeats
XM_005255770.3 → XP_005255827.1 cadherin-16 isoform X3

UniProtKB/TrEMBL

H3BSG2

Conserved Domains (1) summary

cd11304
Location:164 → 267

Cadherin_repeat; Cadherin tandem repeat domain