CDH18

cadherin 18, the group of Type II classical cadherins

Basic information

Region (hg38): 5:19471295-20575873

Links

ENSG00000145526 ∙ NCBI:1016 ∙ OMIM:603019 ∙ HGNC:1757 ∙ Uniprot:Q13634 ∙ 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 CDH18 gene.

• Inborn genetic diseases (22 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH18 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	2
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	2

Variants in CDH18

This is a list of pathogenic ClinVar variants found in the CDH18 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-19473277-A-C		not specified	Uncertain significance (May 05, 2023)
5-19473326-G-A		not specified	Uncertain significance (Feb 14, 2023)
5-19473351-T-C		not specified	Uncertain significance (May 10, 2022)
5-19473658-T-G		CDH18-related disorder	Likely benign (Aug 29, 2023)
5-19473681-T-C		not specified	Uncertain significance (Nov 05, 2021)
5-19473689-C-T		not specified	Uncertain significance (Mar 07, 2024)
5-19483339-G-C		not specified	Uncertain significance (Jul 26, 2022)
5-19483409-C-T		not specified	Uncertain significance (May 03, 2023)
5-19483510-C-G		not specified	Uncertain significance (Jun 22, 2023)
5-19503056-C-A		not specified	Uncertain significance (May 04, 2023)
5-19503069-G-T		not specified	Uncertain significance (Oct 18, 2021)
5-19520685-A-G		not specified	Uncertain significance (Dec 20, 2023)
5-19520709-T-G		not specified	Uncertain significance (Nov 18, 2022)
5-19520710-C-T		not specified	Uncertain significance (Apr 07, 2022)
5-19520752-T-G		CDH18-related disorder	Likely benign (Apr 15, 2022)
5-19520765-C-A		not specified	Uncertain significance (Aug 14, 2023)
5-19543937-C-A		not specified	Uncertain significance (Jul 26, 2022)
5-19544003-T-A		not specified	Uncertain significance (Sep 06, 2022)
5-19571594-G-C		not specified	Uncertain significance (Apr 26, 2023)
5-19571631-C-T		not specified	Uncertain significance (Jul 14, 2022)
5-19571674-A-C			Benign (Dec 31, 2019)
5-19571751-A-C		not specified	Uncertain significance (Oct 26, 2022)
5-19571762-C-T		not specified	Uncertain significance (Jun 18, 2021)
5-19591065-A-G		Childhood apraxia of speech	Uncertain significance (Apr 27, 2016)
5-19591134-T-G		not specified	Uncertain significance (Jan 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH18	protein_coding	protein_coding	ENST00000507958	11	1102923

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.215	0.785	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.808	395	443	0.892	0.0000233	5192
Missense in Polyphen		136	193.47	0.70294		2271
Synonymous	0.0709	162	163	0.993	0.00000914	1555
Loss of Function	3.78	7	28.9	0.242	0.00000129	397

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

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: 0.123

Intolerance Scores

• loftool: 0.357
• rvis_EVS: -1.22
• rvis_percentile_EVS: 5.6

Haploinsufficiency Scores

• pHI: 0.542
• hipred: Y
• hipred_score: 0.543
• ghis: 0.646

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.794

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh18
• Phenotype: homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

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;integral component of membrane;catenin complex
• Molecular function: calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding