CDHR3

protein-coding

cadherin related family member 3, the group of Cadherin related

Gene summary

Predicted to enable beta-catenin binding activity and cadherin binding activity. Predicted to be involved in several processes, including calcium-dependent cell-cell adhesion; cell-cell adhesion mediated by cadherin; and cell-cell junction organization. Located in plasma membrane. Implicated in allergic disease (multiple); bacterial infectious disease; bronchial disease (multiple); and obstructive lung disease. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_152750.5

Inheritance

—

ClinVar variants

P:3U:132B:27

Top phenotype

Susceptibility to nonsyndromic otitis media

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr7:105,876,796-106,036,432

External References & Databases

Ensembl (ENSG00000128536)

Transcript & Mutation Effects

hg38 • Region Span ~159.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDHR3 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 136

not providedTotal: 13

Susceptibility to nonsyndromic otitis mediaTotal: 7

Primary ciliary dyskinesiaTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152750.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	4 clinvar	2 clinvar	7
missense			127 clinvar	21 clinvar		148
nonsense		1 clinvar				1
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)		1 clinvar	3 clinvar			4
Total	0	3	132	25	2	162

Highest pathogenic variant AF is 0.00055310974

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152750.5	RefSeq	NP_689963.2	19	MANE Select
ENST00000317716.14	Ensembl	ENSP00000325954.9	19	MANE Select
NM_001301161.2	RefSeq	NP_001288090.1	17	Standard
ENST00000466045.1	Ensembl	ENSP00000419017.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

virus receptor activity
calcium ion binding
cytoskeletal protein binding
protein homodimerization activity
cadherin binding

Cellular Component

plasma membrane
cell-cell adherens junction
cell surface
integral component of membrane
catenin complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317716
Coding exons: 19
Length: 159636
Individuals with no LoFs: 124248
Homozygous LoFs: 1
Heterozygous LoFs: 395
Defined: 124644
p: 0.00159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.130	486	478	1.02	0.0000247	5772
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0021	0.0020	notable
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0056	0.0055	notable
Finnish	0.0023	0.0023	notable
European (Non-Finnish)	0.0014	0.0013	notable
South Asian	0.00080	0.00072	rare
Other	0.00050	0.00050	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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