CDH10

cadherin 10, the group of Type II classical cadherins

Basic information

Region (hg38): 5:24487100-24644978

Links

ENSG00000040731 ∙ NCBI:1008 ∙ OMIM:604555 ∙ HGNC:1749 ∙ Uniprot:Q9Y6N8 ∙ 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 CDH10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH10 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				1	3	4
missense			28	1		29
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	28	2	3

Variants in CDH10

This is a list of pathogenic ClinVar variants found in the CDH10 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-24487733-C-T		not specified	Uncertain significance (Aug 30, 2021)
5-24487787-A-G		not specified	Uncertain significance (Jun 05, 2024)
5-24487800-T-C		not specified	Uncertain significance (Mar 19, 2024)
5-24487962-T-C		not specified	Uncertain significance (Dec 17, 2023)
5-24487988-A-G		not specified	Uncertain significance (Dec 03, 2021)
5-24488011-G-A			Benign (May 18, 2018)
5-24488026-C-G		not specified	Uncertain significance (May 11, 2022)
5-24488086-T-G		not specified	Uncertain significance (Apr 28, 2023)
5-24488145-C-T			Uncertain significance (-)
5-24488150-A-G		not specified	Uncertain significance (Mar 01, 2024)
5-24491577-C-T			Likely benign (Dec 01, 2022)
5-24491671-T-C			Uncertain significance (-)
5-24491702-T-C		not specified	Uncertain significance (Feb 21, 2024)
5-24492827-C-G		not specified	Uncertain significance (Sep 12, 2023)
5-24492852-G-A		not specified	Uncertain significance (Feb 15, 2023)
5-24492916-T-C		not specified	Uncertain significance (Jun 04, 2024)
5-24498472-C-T		not specified	Uncertain significance (Jun 09, 2022)
5-24498497-G-A			Likely benign (Dec 01, 2022)
5-24498506-C-T			Benign (Dec 31, 2019)
5-24498519-T-C			Uncertain significance (-)
5-24509569-A-C		not specified	Uncertain significance (Dec 07, 2021)
5-24509581-A-G		not specified	Likely benign (Sep 12, 2023)
5-24509749-C-T		not specified	Uncertain significance (May 23, 2023)
5-24509800-C-T		not specified	Uncertain significance (Jun 16, 2023)
5-24509803-C-T		not specified	Uncertain significance (May 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH10	protein_coding	protein_coding	ENST00000264463	11	157879

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.294	0.706	125720	0	27	125747	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.31	301	437	0.689	0.0000233	5176
Missense in Polyphen		130	212.96	0.61045		2486
Synonymous	0.173	160	163	0.983	0.00000936	1553
Loss of Function	4.18	8	34.5	0.232	0.00000210	385

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000215
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000639	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000546	0.000490
Other	0.00	0.00

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: Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.553
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.33

Haploinsufficiency Scores

• pHI: 0.420
• hipred: Y
• hipred_score: 0.740
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.913

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh10

Gene ontology

• Biological process: cell morphogenesis;cell-cell junction assembly;homophilic cell adhesion via plasma membrane adhesion molecules;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;adherens junction organization;cell-cell adhesion mediated by cadherin;cell-cell adhesion
• Cellular component: plasma membrane;cell-cell adherens junction;cell surface;catenin complex;glutamatergic synapse;GABA-ergic synapse;integral component of presynaptic active zone membrane;integral component of postsynaptic specialization membrane
• Molecular function: calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding