CDH20

cadherin 20, the group of Type II classical cadherins

Basic information

Region (hg38): 18:61333430-61555779

Links

ENSG00000101542NCBI:28316OMIM:605807HGNC:1760Uniprot:Q9HBT6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDH20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH20 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
3
clinvar
1
clinvar
4
missense
29
clinvar
29
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 29 3 1

Variants in CDH20

This is a list of pathogenic ClinVar variants found in the CDH20 region.

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

Position Type Phenotype Significance ClinVar
18-61490576-G-A not specified Uncertain significance (Oct 09, 2024)3488875
18-61490639-C-T not specified Uncertain significance (Dec 16, 2023)3141191
18-61490654-C-T not specified Uncertain significance (Apr 08, 2024)3265239
18-61490670-A-G Benign (Mar 02, 2018)710667
18-61490708-A-G not specified Uncertain significance (Jan 04, 2024)3141186
18-61490770-A-G not specified Uncertain significance (May 30, 2023)2552788
18-61490781-C-A not specified Uncertain significance (Nov 08, 2022)2220179
18-61499266-C-T Likely benign (Jan 01, 2023)2648771
18-61499303-C-A not specified Uncertain significance (Sep 14, 2021)2347718
18-61499361-C-T not specified Uncertain significance (Aug 28, 2023)2599160
18-61499363-G-A not specified Uncertain significance (Sep 20, 2023)3141189
18-61499381-G-A not specified Uncertain significance (Oct 22, 2024)3488873
18-61500448-G-A not specified Uncertain significance (Sep 26, 2024)3488879
18-61502956-T-C not specified Uncertain significance (Oct 21, 2021)2256322
18-61502962-G-A not specified Uncertain significance (Nov 09, 2023)3141190
18-61503109-G-A not specified Uncertain significance (Jun 07, 2024)3265235
18-61507389-T-G not specified Uncertain significance (Apr 06, 2024)3265240
18-61507420-G-A not specified Uncertain significance (Mar 25, 2022)2370233
18-61507422-C-T Likely benign (Jan 01, 2023)2648772
18-61507427-G-C not specified Uncertain significance (Nov 19, 2022)2328499
18-61507494-T-C Likely benign (Jan 01, 2023)2648773
18-61528073-C-T not specified Uncertain significance (Jul 28, 2021)2239827
18-61528140-G-C not specified Uncertain significance (Jun 10, 2022)2295234
18-61528157-C-T not specified Uncertain significance (Jan 23, 2024)3141185
18-61528163-G-C not specified Uncertain significance (Jun 02, 2024)3265242

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CDH20protein_codingprotein_codingENST00000262717 11222192
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4590.5411257240241257480.0000954
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.384124990.8260.00003115280
Missense in Polyphen145200.870.721842162
Synonymous0.1122102120.9900.00001591566
Loss of Function4.09732.00.2190.00000145369

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002470.000246
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.0001920.000185
European (Non-Finnish)0.0001000.0000967
Middle Eastern0.0001090.000109
South Asian0.00006550.0000653
Other0.0001630.000163

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.;

Recessive Scores

pRec
0.0974

Intolerance Scores

loftool
0.230
rvis_EVS
-0.62
rvis_percentile_EVS
17.4

Haploinsufficiency Scores

pHI
0.411
hipred
Y
hipred_score
0.783
ghis
0.535

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.185

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cdh20
Phenotype

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