CDHR4

cadherin related family member 4, the group of Cadherin related

Basic information

Region (hg38): 3:49790732-49799873

Previous symbols: [ "CDH29" ]

Links

ENSG00000187492 ∙ NCBI:389118 ∙ ∙ HGNC:34527 ∙ Uniprot:A6H8M9 ∙ 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 CDHR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDHR4 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			63	9		72
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	63	10	0

Variants in CDHR4

This is a list of pathogenic ClinVar variants found in the CDHR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49790882-C-T		not specified	Uncertain significance (Mar 20, 2023)
3-49791447-C-T		not specified	Uncertain significance (Jun 22, 2021)
3-49791715-A-G		not specified	Uncertain significance (Dec 06, 2022)
3-49791720-C-T		not specified	Uncertain significance (Nov 01, 2022)
3-49791758-G-A		not specified	Uncertain significance (Mar 28, 2023)
3-49791776-C-T		not specified	Uncertain significance (Nov 23, 2022)
3-49791801-G-C		not specified	Uncertain significance (Jun 01, 2023)
3-49791918-G-A		not specified	Uncertain significance (Sep 17, 2021)
3-49791925-C-G		not specified	Uncertain significance (Nov 27, 2024)
3-49791933-C-T		not specified	Uncertain significance (Nov 24, 2024)
3-49791950-C-G		not specified	Uncertain significance (Dec 15, 2023)
3-49792499-G-T		not specified	Uncertain significance (Dec 10, 2024)
3-49792525-G-T		not specified	Uncertain significance (Oct 20, 2024)
3-49792559-G-T		not specified	Uncertain significance (Feb 26, 2025)
3-49792600-G-A		not specified	Likely benign (Jun 28, 2024)
3-49792942-G-A		not specified	Likely benign (Jun 02, 2024)
3-49792958-C-T		not specified	Uncertain significance (Jan 24, 2025)
3-49793048-G-C		not specified	Uncertain significance (Feb 02, 2022)
3-49793059-C-T		not specified	Uncertain significance (Mar 30, 2024)
3-49793167-C-G		not specified	Uncertain significance (Jan 16, 2024)
3-49793193-T-C		not specified	Uncertain significance (Aug 28, 2023)
3-49793235-A-G		not specified	Uncertain significance (Jul 14, 2024)
3-49793241-C-T		not specified	Likely benign (Feb 07, 2023)
3-49793295-G-A		not specified	Uncertain significance (Mar 11, 2022)
3-49793631-G-C		not specified	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDHR4	protein_coding	protein_coding	ENST00000412678	19	9104

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.77e-13	0.727	124615	0	9	124624	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.18	319	449	0.710	0.0000254	5048
Missense in Polyphen		54	98.851	0.54628		1233
Synonymous	1.69	155	184	0.842	0.0000107	1640
Loss of Function	1.72	25	36.1	0.692	0.00000164	412

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000523	0.0000464
European (Non-Finnish)	0.0000179	0.0000177
Middle Eastern	0.0000556	0.0000556
South Asian	0.000189	0.000163
Other	0.00	0.00

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 (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.563
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

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: Cdhr4

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules
• Cellular component: integral component of plasma membrane
• Molecular function: calcium ion binding