CDH16

cadherin 16, the group of 7D cadherins

Basic information

Region (hg38): 16:66908122-66918917

Links

ENSG00000166589 ∙ NCBI:1014 ∙ OMIM:603118 ∙ HGNC:1755 ∙ Uniprot:O75309 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDH16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH16 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			75	10	1	86
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	75	12	2

Variants in CDH16

This is a list of pathogenic ClinVar variants found in the CDH16 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-66908415-C-T		not specified	Uncertain significance (Nov 14, 2024)
16-66908438-T-C		not specified	Uncertain significance (Oct 29, 2021)
16-66908457-T-G		not specified	Uncertain significance (Dec 28, 2024)
16-66908465-G-A		not specified	Uncertain significance (Nov 21, 2023)
16-66909269-A-G		not specified	Uncertain significance (Oct 08, 2024)
16-66909314-G-A		not specified	Uncertain significance (Sep 12, 2024)
16-66909321-T-C		not specified	Uncertain significance (Dec 12, 2022)
16-66909345-G-A		not specified	Uncertain significance (Dec 25, 2024)
16-66909345-G-T		not specified	Uncertain significance (Nov 02, 2023)
16-66909363-C-T		not specified	Uncertain significance (Sep 25, 2023)
16-66909998-G-T		not specified	Uncertain significance (Oct 04, 2024)
16-66910015-T-C		not specified	Uncertain significance (Dec 20, 2022)
16-66910039-A-G		not specified	Uncertain significance (Feb 25, 2025)
16-66910046-C-T		not specified	Uncertain significance (Nov 10, 2024)
16-66910277-C-T			Benign (Dec 31, 2019)
16-66910278-G-A		not specified	Uncertain significance (Dec 04, 2024)
16-66910280-C-A		not specified	Uncertain significance (Jun 11, 2024)
16-66910295-G-A		not specified	Uncertain significance (Nov 15, 2024)
16-66910314-T-C		not specified	Likely benign (Jan 30, 2024)
16-66910341-C-T		not specified	Uncertain significance (Oct 20, 2024)
16-66910391-C-T		not specified	Uncertain significance (Jan 08, 2025)
16-66910422-G-A		not specified	Uncertain significance (Nov 24, 2024)
16-66910448-G-A		not specified	Uncertain significance (Jun 04, 2024)
16-66910449-G-A		not specified	Uncertain significance (Mar 19, 2024)
16-66910478-G-A		not specified	Likely benign (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH16	protein_coding	protein_coding	ENST00000299752	17	10863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.65e-25	0.000519	125635	1	112	125748	0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.302	512	493	1.04	0.0000277	5345
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00229	0.00192
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000416	0.000404
Middle Eastern	0.000163	0.000163
South Asian	0.000493	0.000457
Other	0.000328	0.000326

dbNSFP

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.
• Pathway: TGF-B Signaling in Thyroid Cells for Epithelial-Mesenchymal Transition (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.949
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.38

Haploinsufficiency Scores

• pHI: 0.0908
• hipred: N
• hipred_score: 0.170
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.106

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh16

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
• Cellular component: integral component of plasma membrane;basolateral plasma membrane;extracellular exosome
• Molecular function: calcium ion binding