CDHR3

cadherin related family member 3, the group of Cadherin related

Basic information

Region (hg38): 7:105876796-106036432

Links

ENSG00000128536 ∙ NCBI:222256 ∙ OMIM:615610 ∙ HGNC:26308 ∙ Uniprot:Q6ZTQ4 ∙ 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 CDHR3 gene.

• not_specified (120 variants)
• not_provided (12 variants)
• Susceptibility_to_nonsyndromic_otitis_media (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDHR3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152750.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	2	5
missense			109	19		128
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	110	22	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDHR3	protein_coding	protein_coding	ENST00000317716	19	159636

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-24	0.000799	124248	1	395	124644	0.00159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.130	486	478	1.02	0.0000247	5772
Missense in Polyphen		139	146.84	0.94661		1899
Synonymous	-0.255	192	188	1.02	0.0000110	1750
Loss of Function	0.186	37	38.2	0.968	0.00000205	448

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00327	0.00313
Ashkenazi Jewish	0.000200	0.000199
East Asian	0.00564	0.00552
Finnish	0.00232	0.00228
European (Non-Finnish)	0.00141	0.00135
Middle Eastern	0.00564	0.00552
South Asian	0.000803	0.000719
Other	0.000501	0.000496

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.

Intolerance Scores

• loftool: 0.957
• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.85

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdhr3

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;viral entry into host cell;cell-cell adhesion
• Cellular component: plasma membrane;cell-cell adherens junction;cell surface;integral component of membrane;catenin complex
• Molecular function: virus receptor activity;calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding