CDH4

cadherin 4, the group of Type I classical cadherins

Basic information

Region (hg38): 20:61252261-61940617

Links

ENSG00000179242

∙ NCBI:1002 ∙ OMIM:603006 ∙ HGNC:1763 ∙ Uniprot:P55283 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

multiple congenital anomalies/dysmorphic syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDH4 gene.

not_specified (135 variants)
CDH4-related_disorder (18 variants)
not_provided (16 variants)
Simplified_gyral_pattern (2 variants)
Neurodevelopmental_disorder (1 variants)
Abnormal_brain_morphology (1 variants)
CDH4-associated_disorder_of_corticaldevelopment (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001794.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				15 clinvar	5 clinvar	20
missense		1 clinvar	137 clinvar	5 clinvar	1 clinvar	144
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	137	20	6

Highest pathogenic variant AF is 6.85134e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH4	protein_coding	protein_coding	ENST00000360469	16	688192

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.743	0.257	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.02	480	622	0.772	0.0000438	5987
Missense in Polyphen		131	229.5	0.5708		2138
Synonymous	-0.879	295	276	1.07	0.0000230	1854
Loss of Function	4.66	8	39.7	0.202	0.00000214	410

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.000164	0.000163
South Asian	0.0000989	0.0000980
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 play an important role in retinal development.;
Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Developmental Biology;CDO in myogenesis;Myogenesis;Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

pRec: 0.143

Intolerance Scores

loftool: 0.252
rvis_EVS: -2.07
rvis_percentile_EVS: 1.62

Haploinsufficiency Scores

pHI: 0.141
hipred: Y
hipred_score: 0.625
ghis: 0.635

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.803

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cdh4
Phenotype: cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; renal/urinary system phenotype;

Zebrafish Information Network

Gene name: cdh4
Affected structure: retinal ganglion cell
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: cell morphogenesis;cell-cell junction assembly;cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;axon guidance;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;adherens junction organization;cell-cell adhesion mediated by cadherin;positive regulation of axon extension;cell-cell adhesion
Cellular component: plasma membrane;integral component of plasma membrane;cell-cell adherens junction;cell surface;catenin complex
Molecular function: calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding