CDHR5

cadherin related family member 5, the group of Cadherin related

Basic information

Region (hg38): 11:616576-626078

Previous symbols: [ "MUCDHL", "MUPCDH" ]

Links

ENSG00000099834 ∙ NCBI:53841 ∙ OMIM:606839 ∙ HGNC:7521 ∙ Uniprot:Q9HBB8 ∙ 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 CDHR5 gene.

• Inborn genetic diseases (75 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDHR5 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					1	1
missense			69	6	1	76
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	69	6	2

Variants in CDHR5

This is a list of pathogenic ClinVar variants found in the CDHR5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-617374-C-T		not specified	Uncertain significance (Jul 20, 2022)
11-617406-G-A		not specified	Uncertain significance (Feb 03, 2022)
11-617407-C-T		not specified	Uncertain significance (Jun 14, 2023)
11-617466-G-A		not specified	Uncertain significance (Jul 16, 2021)
11-617467-C-T		not specified	Likely benign (May 01, 2022)
11-617482-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-617491-C-G		not specified	Uncertain significance (Sep 16, 2021)
11-617520-G-A		not specified	Uncertain significance (Feb 28, 2023)
11-617533-C-T		not specified	Uncertain significance (May 13, 2022)
11-617541-C-T		not specified	Uncertain significance (Dec 27, 2022)
11-617574-G-T		not specified	Uncertain significance (May 24, 2023)
11-617584-C-T		not specified	Uncertain significance (Jan 03, 2024)
11-617598-G-A		not specified	Uncertain significance (Aug 17, 2021)
11-617620-C-T		not specified	Likely benign (May 10, 2022)
11-617626-G-A		not specified	Uncertain significance (May 05, 2023)
11-617673-G-A		not specified	Uncertain significance (Oct 31, 2022)
11-617685-T-A		not specified	Uncertain significance (Sep 16, 2021)
11-617688-T-G		not specified	Likely benign (Sep 16, 2021)
11-617704-C-T		not specified	Uncertain significance (Jan 07, 2022)
11-617709-G-A		not specified	Uncertain significance (Feb 23, 2023)
11-617739-G-A		not specified	Uncertain significance (Feb 27, 2023)
11-617744-G-T		not specified	Uncertain significance (Nov 12, 2021)
11-617969-G-C		not specified	Uncertain significance (Jan 06, 2023)
11-618042-G-A		not specified	Uncertain significance (Jul 11, 2023)
11-618088-G-A		not specified	Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDHR5	protein_coding	protein_coding	ENST00000358353	15	9514

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.74e-19	0.00758	125632	1	109	125742	0.000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.20	621	542	1.15	0.0000354	5322
Missense in Polyphen		244	230.23	1.0598		2275
Synonymous	-4.12	333	250	1.33	0.0000191	1871
Loss of Function	0.329	29	31.0	0.936	0.00000147	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00150	0.00147
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000330	0.000326
Finnish	0.0000648	0.0000462
European (Non-Finnish)	0.000538	0.000519
Middle Eastern	0.000330	0.000326
South Asian	0.000468	0.000425
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Intermicrovillar adhesion molecule that forms, via its extracellular domain, calcium-dependent heterophilic complexes with CDHR2 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. {ECO:0000269|PubMed:24725409}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.811
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.06

Haploinsufficiency Scores

• pHI: 0.0919
• hipred: N
• hipred_score: 0.146

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	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cdhr5

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;cell differentiation;regulation of microvillus length;intermicrovillar adhesion
• Cellular component: clathrin-coated pit;apical plasma membrane;brush border membrane;microvillus membrane;spanning component of plasma membrane;extracellular exosome
• Molecular function: calcium ion binding;protein binding;beta-catenin binding;cell adhesion molecule binding