CDHR3

cadherin related family member 3, the group of Cadherin related

Basic information

Region (hg38): 7:105876795-106036432

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.

• Inborn genetic diseases (41 variants)
• not provided (12 variants)
• Susceptibility to nonsyndromic otitis media (4 variants)
• not specified (1 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.

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	2	5
missense			35	11		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	35	14	2

Variants in CDHR3

This is a list of pathogenic ClinVar variants found in the CDHR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-105974844-G-C		not specified	Uncertain significance (Jan 31, 2024)
7-105974880-C-T		not specified	Likely benign (Jun 29, 2022)
7-105974924-A-C		not specified	Uncertain significance (Jul 26, 2022)
7-105981016-A-G		not specified	Uncertain significance (May 06, 2022)
7-105981049-G-T		not specified	Uncertain significance (Dec 18, 2023)
7-105984200-C-A		not specified	Uncertain significance (Jun 10, 2022)
7-105994770-C-A		not specified	Uncertain significance (Jun 11, 2021)
7-105994839-A-G		not specified	Uncertain significance (Apr 25, 2023)
7-105996263-G-A		Susceptibility to nonsyndromic otitis media • not specified	Uncertain significance (Aug 02, 2021)
7-105996270-T-G		not specified	Uncertain significance (Sep 29, 2023)
7-105996280-T-C			Likely benign (May 01, 2022)
7-105996332-G-A		not specified	Uncertain significance (Mar 31, 2023)
7-105996344-C-T		not specified	Uncertain significance (Jan 17, 2023)
7-105996345-G-A		not specified	Likely benign (Jan 04, 2022)
7-106001506-C-A		not specified	Uncertain significance (Apr 08, 2022)
7-106001584-T-C		not specified	Uncertain significance (Sep 29, 2023)
7-106001586-A-G		not specified	Uncertain significance (Sep 29, 2023)
7-106004617-C-A		not specified	Uncertain significance (Jan 06, 2023)
7-106004618-G-A		not specified	Likely benign (Jul 19, 2023)
7-106004618-G-T		not specified	Uncertain significance (Jan 06, 2023)
7-106004646-C-T			Benign (Dec 31, 2019)
7-106004676-G-T		not specified	Uncertain significance (Aug 05, 2023)
7-106012870-C-T		not specified	Uncertain significance (Jun 05, 2023)
7-106012871-C-T		Susceptibility to nonsyndromic otitis media	Uncertain significance (Feb 01, 2013)
7-106012942-C-T		Susceptibility to nonsyndromic otitis media	Uncertain significance (Feb 01, 2013)

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