CDH13

cadherin 13, the group of Major cadherins|MicroRNA protein coding host genes

Basic information

Region (hg38): 16:82626964-83800640

Links

ENSG00000140945 ∙ NCBI:1012 ∙ OMIM:601364 ∙ HGNC:1753 ∙ Uniprot:P55290 ∙ 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 CDH13 gene.

• not provided (63 variants)
• Inborn genetic diseases (40 variants)
• not specified (10 variants)
• CDH13-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH13 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				5	8	13
missense			39	8	1	48
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding					43	43
Total	0	0	40	13	52

Variants in CDH13

This is a list of pathogenic ClinVar variants found in the CDH13 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-82627104-A-G		not specified	Likely benign (May 24, 2023)
16-82627118-T-C		not specified	Uncertain significance (Aug 30, 2021)
16-82627145-A-G		CDH13-related disorder	Likely benign (Feb 19, 2019)
16-82627349-T-C			Benign (Jun 21, 2021)
16-82639442-C-T		not specified	Benign (-)
16-82639464-A-G		CDH13-related disorder	Benign (Jun 05, 2020)
16-82639485-T-G		not specified	Benign (-)
16-82858053-A-G			Benign (Jun 18, 2021)
16-82858291-G-A			Benign (Jun 18, 2021)
16-82858425-C-A		not specified	Uncertain significance (Jan 24, 2023)
16-82858432-A-G		not specified	Benign (Jun 10, 2021)
16-82858467-C-G		not specified	Uncertain significance (Jun 18, 2021)
16-83031764-G-C			Benign (Jun 18, 2021)
16-83031798-T-C			Benign (Jun 18, 2021)
16-83031886-G-C			Benign (Jun 18, 2021)
16-83032046-G-A		not specified	Likely benign (Mar 20, 2023)
16-83032058-C-G		not specified	Uncertain significance (Jan 17, 2024)
16-83032059-G-A		not specified	Benign (-)
16-83032085-A-T		not specified	Uncertain significance (May 26, 2023)
16-83032090-G-A		not specified	Likely benign (Dec 28, 2022)
16-83032111-A-T		not specified	Uncertain significance (Sep 27, 2022)
16-83032118-C-T		not specified	Uncertain significance (Apr 20, 2023)
16-83032124-GC-G		CDH13-related disorder	Uncertain significance (Jun 16, 2023)
16-83032130-C-G		not specified	Uncertain significance (Nov 06, 2023)
16-83032148-G-A		not specified	Uncertain significance (Feb 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH13	protein_coding	protein_coding	ENST00000268613	15	1169797

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000706	0.999	124641	0	13	124654	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.533	480	448	1.07	0.0000253	4971
Missense in Polyphen		125	177.7	0.70344		1989
Synonymous	-5.05	268	181	1.48	0.0000114	1525
Loss of Function	3.29	11	30.7	0.359	0.00000148	371

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000693	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000998	0.0000973
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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. May act as a negative regulator of neural cell growth. {ECO:0000269|PubMed:10737605}.
• Pathway: Pathways in clear cell renal cell carcinoma;Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.403

Intolerance Scores

• loftool: 0.493
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.320
• hipred: Y
• hipred_score: 0.554
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0882

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh13
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: mitotic cell cycle;cell morphogenesis;positive regulation of endothelial cell proliferation;positive regulation of cell-matrix adhesion;sprouting angiogenesis;cell-cell junction assembly;homophilic cell adhesion via plasma membrane adhesion molecules;negative regulation of cell adhesion;Rho protein signal transduction;negative regulation of cell population proliferation;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;Rac protein signal transduction;lamellipodium assembly;regulation of endocytosis;positive regulation of cell migration;adherens junction organization;regulation of epidermal growth factor receptor signaling pathway;endothelial cell migration;keratinocyte proliferation;cell-cell adhesion mediated by cadherin;positive regulation of transcription by RNA polymerase II;positive regulation of smooth muscle cell proliferation;positive regulation of calcium-mediated signaling;positive regulation of positive chemotaxis;localization within membrane;low-density lipoprotein particle mediated signaling;cell-cell adhesion
• Cellular component: extracellular region;extracellular space;cytoplasm;plasma membrane;caveola;cell-cell adherens junction;focal adhesion;external side of plasma membrane;cell surface;catenin complex;anchored component of membrane;neuron projection;perinuclear region of cytoplasm;collagen-containing extracellular matrix;extracellular exosome;GABA-ergic synapse
• Molecular function: calcium ion binding;cytoskeletal protein binding;low-density lipoprotein particle binding;protein homodimerization activity;cadherin binding;adiponectin binding;lipoprotein particle binding