CDHR2

cadherin related family member 2, the group of Cadherin related

Basic information

Region (hg38): 5:176542511-176595974

Previous symbols: [ "PCDH24" ]

Links

ENSG00000074276 ∙ NCBI:54825 ∙ OMIM:619713 ∙ HGNC:18231 ∙ Uniprot:Q9BYE9 ∙ 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 CDHR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDHR2 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		6
missense			78	9		87
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	78	15	0

Variants in CDHR2

This is a list of pathogenic ClinVar variants found in the CDHR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-176565690-C-T		not specified	Uncertain significance (Dec 01, 2022)
5-176565711-C-T			Uncertain significance (Feb 08, 2023)
5-176568722-C-T		not specified	Uncertain significance (Oct 10, 2023)
5-176568739-G-T		not specified	Likely benign (Jan 03, 2022)
5-176568764-G-A		not specified	Likely benign (Aug 22, 2023)
5-176568794-C-G		not specified	Uncertain significance (Aug 09, 2021)
5-176568802-C-T			Likely benign (Nov 01, 2022)
5-176568984-A-G		not specified	Uncertain significance (Dec 07, 2021)
5-176571263-C-T			Likely benign (Mar 01, 2022)
5-176571264-G-A		not specified	Uncertain significance (Dec 07, 2021)
5-176571294-A-C		not specified	Uncertain significance (Mar 18, 2024)
5-176574168-A-T		not specified	Uncertain significance (Dec 08, 2023)
5-176575121-G-A		not specified	Uncertain significance (Jun 03, 2024)
5-176575322-T-G		not specified	Uncertain significance (Jun 29, 2023)
5-176575398-C-T		not specified	Uncertain significance (Jun 24, 2022)
5-176575522-C-T		not specified	Uncertain significance (Nov 05, 2021)
5-176575579-C-T		not specified	Uncertain significance (Jul 15, 2021)
5-176575730-C-A		not specified	Uncertain significance (Apr 18, 2023)
5-176575754-G-T		not specified	Uncertain significance (May 13, 2024)
5-176575760-A-T		not specified	Uncertain significance (Dec 28, 2023)
5-176575763-G-C		not specified	Uncertain significance (May 16, 2024)
5-176575793-G-C		not specified	Uncertain significance (Dec 13, 2023)
5-176575979-G-A		not specified	Uncertain significance (Mar 15, 2024)
5-176576087-G-A		not specified	Uncertain significance (Dec 22, 2023)
5-176576117-G-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDHR2	protein_coding	protein_coding	ENST00000510636	31	53464

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.43e-20	0.947	125556	0	192	125748	0.000764

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.372	767	797	0.963	0.0000490	8519
Missense in Polyphen		218	241.71	0.90192		2772
Synonymous	-0.913	393	371	1.06	0.0000268	2707
Loss of Function	2.53	41	62.6	0.655	0.00000326	663

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00245	0.00245
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00104	0.00103
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000830	0.000818
Middle Eastern	0.00104	0.00103
South Asian	0.000622	0.000555
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Intermicrovillar adhesion molecule that forms, via its extracellular domain, calcium-dependent heterophilic complexes with CDHR5 on adjacent microvilli. Thereby, controls the packing of microvilli at the apical membrane of epithelial cells. Through its cytoplasmic domain, interacts with microvillus cytoplasmic proteins to form the intermicrovillar adhesion complex/IMAC. This complex plays a central role in microvilli and epithelial brush border differentiation (PubMed:24725409). May also play a role in cell-cell adhesion and contact inhibition in epithelial cells (PubMed:12117771). {ECO:0000269|PubMed:12117771, ECO:0000269|PubMed:24725409}.

Recessive Scores

• pRec: 0.0898

Intolerance Scores

• loftool: 0.799
• rvis_EVS: 0.96
• rvis_percentile_EVS: 90.12

Haploinsufficiency Scores

• pHI: 0.0920
• hipred: N
• hipred_score: 0.280

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdhr2

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;epithelial cell differentiation;regulation of microvillus length;cell-cell adhesion mediated by cadherin;negative regulation of cell growth involved in contact inhibition;intermicrovillar adhesion
• Cellular component: brush border;apical plasma membrane;cell junction;brush border membrane;microvillus membrane;spanning component of plasma membrane;extracellular exosome
• Molecular function: calcium ion binding;protein binding;cell adhesion molecule binding