CDH8

cadherin 8, the group of Type II classical cadherins

Basic information

Region (hg38): 16:61647242-62037035

Links

ENSG00000150394 ∙ NCBI:1006 ∙ OMIM:603008 ∙ HGNC:1767 ∙ Uniprot:P55286 ∙ 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 CDH8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH8 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				6	2	8
missense			29	1		30
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	7	2

Variants in CDH8

This is a list of pathogenic ClinVar variants found in the CDH8 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-61653612-GTTTC-G			Uncertain significance (Mar 09, 2020)
16-61653750-C-G			Uncertain significance (Jun 02, 2021)
16-61653798-G-A		not specified	Uncertain significance (Jun 17, 2024)
16-61653816-T-C		not specified	Uncertain significance (Jan 04, 2024)
16-61654007-G-A			Benign/Likely benign (Aug 01, 2022)
16-61654011-C-T		not specified	Uncertain significance (Jun 17, 2024)
16-61654012-G-A			Likely benign (Dec 31, 2019)
16-61654074-C-T		not specified	Uncertain significance (May 29, 2024)
16-61654097-G-A			Benign (Feb 25, 2018)
16-61655497-T-C		not specified	Uncertain significance (Mar 01, 2023)
16-61655536-C-T		not specified	Uncertain significance (Mar 14, 2023)
16-61655549-A-T		not specified	Uncertain significance (Oct 26, 2022)
16-61655573-A-C		not specified	Uncertain significance (Jan 30, 2024)
16-61713909-T-C		not specified	Uncertain significance (May 21, 2024)
16-61713919-T-G		not specified	Uncertain significance (Aug 02, 2022)
16-61727100-G-A			Likely benign (Aug 01, 2022)
16-61727127-C-T			Likely benign (May 04, 2018)
16-61789370-T-A		not specified	Uncertain significance (Jan 24, 2024)
16-61789382-C-A		not specified	Uncertain significance (Dec 13, 2022)
16-61789473-G-A			Benign (Nov 26, 2018)
16-61817526-A-C		not specified	Uncertain significance (Mar 17, 2023)
16-61817532-G-A			Likely benign (Jun 05, 2018)
16-61817615-C-T		not specified	Uncertain significance (Sep 17, 2021)
16-61817626-G-A		not specified	Uncertain significance (Feb 06, 2024)
16-61820936-C-T		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH8	protein_coding	protein_coding	ENST00000577390	11	389794

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0119	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.42	315	461	0.683	0.0000253	5266
Missense in Polyphen		107	196.3	0.54508		2198
Synonymous	-0.592	185	175	1.06	0.0000102	1574
Loss of Function	4.49	4	31.0	0.129	0.00000165	381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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: Ectoderm Differentiation;Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.194
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

• pHI: 0.767
• hipred: Y
• hipred_score: 0.774
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.815

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh8
• 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); vision/eye 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cell morphogenesis;cell-cell junction assembly;cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;response to cold;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;adherens junction organization;synaptic transmission, glutamatergic;cell-cell adhesion mediated by cadherin;regulation of synapse organization;cell-cell adhesion
• Cellular component: plasma membrane;cell-cell adherens junction;cell surface;integral component of membrane;catenin complex;synaptic cleft;axon terminus;synaptic membrane;glutamatergic synapse
• Molecular function: calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding