CDH16

protein-coding

cadherin 16, the group of 7D cadherins

Gene 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]

MANE transcript

NM_004062.4

Inheritance

—

ClinVar variants

U:141B:20

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr16:66,908,122-66,918,917

External References & Databases

Ensembl (ENSG00000166589)

Transcript & Mutation Effects

hg38 • Region Span ~10.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDH16 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 154

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004062.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar	1 clinvar	4
missense			138 clinvar	16 clinvar	1 clinvar	155
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	141	18	2	161

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 75 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004062.4	RefSeq	NP_004053.1	17	MANE Select
ENST00000299752.9	Ensembl	ENSP00000299752.4	17	MANE Select
NM_001204744.2	RefSeq	NP_001191673.1	17	Standard
NM_001204745.2	RefSeq	NP_001191674.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TGF-B Signaling in Thyroid Cells for Epithelial-Mesenchymal Transition

Biological Process

cell adhesion
homophilic cell adhesion via plasma membrane adhesion molecules
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules

Molecular Function

calcium ion binding

Cellular Component

integral component of plasma membrane
basolateral plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000299752
Coding exons: 17
Length: 10863
Individuals with no LoFs: 125635
Homozygous LoFs: 1
Heterozygous LoFs: 112
Defined: 125748
p: 0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.302	512	493	1.04	0.0000277	5345
Missense (PolyPhen)		133	145.34	0.91511		1712
Synonymous	0.285	204	209	0.975	0.0000130	1747
Loss of Function	0.130	38	38.9	0.978	0.00000203	408

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0015	0.0011	notable
Latino/Admixed American	0.00081	0.00081	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00042	0.00040	rare
South Asian	0.00049	0.00046	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.;

Recessive Scores

pRec: 0.128

Intolerance Scores

LoFtool: 0.949
RVIS EVS: -0.95
RVIS percentile EVS: 9.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.106

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium