CDH19

cadherin 19, the group of Type II classical cadherins

Basic information

Region (hg38): 18:66501083-66604138

Links

ENSG00000071991 ∙ NCBI:28513 ∙ OMIM:603016 ∙ HGNC:1758 ∙ Uniprot:Q9H159 ∙ 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 CDH19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH19 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	3	5
missense			50	7	6	63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1		1
Total	0	0	51	9	9

Variants in CDH19

This is a list of pathogenic ClinVar variants found in the CDH19 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-66504877-C-T		not specified	Uncertain significance (Apr 08, 2022)
18-66504924-A-G		not specified	Uncertain significance (May 04, 2022)
18-66504951-C-A		CDH19-related disorder	Benign (Feb 25, 2019)
18-66504997-C-T		CDH19-related disorder	Benign (Aug 01, 2019)
18-66505069-C-T		not specified	Uncertain significance (Feb 22, 2023)
18-66505086-T-A		not specified	Uncertain significance (Jan 02, 2024)
18-66505173-G-T		CDH19-related disorder	Benign (Apr 30, 2019)
18-66505195-C-T		CDH19-related disorder	Likely benign (May 15, 2019)
18-66505222-T-C		not specified	Uncertain significance (Mar 14, 2023)
18-66505261-G-T		not specified	Uncertain significance (Sep 26, 2022)
18-66505269-C-T		not specified	Uncertain significance (Oct 03, 2022)
18-66505277-T-G		not specified	Uncertain significance (May 25, 2022)
18-66509020-A-C		not specified	Uncertain significance (Oct 06, 2021)
18-66509032-G-A		CDH19-related disorder	Benign (Aug 08, 2019)
18-66509048-C-G		not specified	Uncertain significance (Aug 31, 2022)
18-66509084-T-C		not specified	Uncertain significance (Mar 18, 2024)
18-66509105-C-T		not specified	Uncertain significance (Jun 09, 2022)
18-66509127-G-A		not specified	Uncertain significance (Jul 08, 2022)
18-66509149-C-T		CDH19-related disorder	Benign (Dec 31, 2019)
18-66509192-G-A		not specified	Uncertain significance (Feb 16, 2023)
18-66511601-T-A		not specified	Uncertain significance (Sep 27, 2022)
18-66529846-T-C		not specified	Uncertain significance (Mar 27, 2023)
18-66529903-G-A		not specified	Uncertain significance (Dec 27, 2023)
18-66529945-G-A		not specified	Uncertain significance (Apr 28, 2022)
18-66529963-T-C		not specified	Uncertain significance (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH19	protein_coding	protein_coding	ENST00000262150	11	103056

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.29e-14	0.158	125631	2	115	125748	0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.708	450	410	1.10	0.0000202	5094
Missense in Polyphen		174	150.14	1.1589		1895
Synonymous	-1.56	170	146	1.16	0.00000763	1431
Loss of Function	1.03	25	31.2	0.801	0.00000149	402

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000859	0.000854
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000502	0.000489
Finnish	0.0000951	0.0000924
European (Non-Finnish)	0.000309	0.000281
Middle Eastern	0.000502	0.000489
South Asian	0.00178	0.00170
Other	0.000164	0.000163

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.

Recessive Scores

• pRec: 0.0956

Intolerance Scores

• loftool: 0.798
• rvis_EVS: 1.4
• rvis_percentile_EVS: 94.75

Haploinsufficiency Scores

• pHI: 0.0414
• hipred: N
• hipred_score: 0.187
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh19
• Phenotype: homeostasis/metabolism phenotype

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;cell-cell adhesion
• Cellular component: plasma membrane;cell-cell adherens junction;cell surface;integral component of membrane;catenin complex
• Molecular function: calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding