CDH9

cadherin 9, the group of Type II classical cadherins

Basic information

Region (hg38): 5:26880596-27121150

Links

ENSG00000113100 ∙ NCBI:1007 ∙ OMIM:609974 ∙ HGNC:1768 ∙ Uniprot:Q9ULB4 ∙ 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 CDH9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH9 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	2
missense			37		2	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	1	3

Variants in CDH9

This is a list of pathogenic ClinVar variants found in the CDH9 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-26881152-T-C		not specified	Uncertain significance (Jan 08, 2024)
5-26881170-T-A		not specified	Uncertain significance (Mar 03, 2022)
5-26881188-C-A		not specified	Uncertain significance (Oct 17, 2023)
5-26881188-C-T		not specified	Uncertain significance (Jan 26, 2022)
5-26881219-C-T		not specified	Uncertain significance (Aug 28, 2023)
5-26881285-C-G		not specified	Uncertain significance (Sep 28, 2022)
5-26881304-C-T			Uncertain significance (-)
5-26881342-C-G		not specified	Uncertain significance (Dec 03, 2021)
5-26881367-T-G		not specified	Uncertain significance (Dec 13, 2022)
5-26881387-A-C		not specified	Uncertain significance (May 12, 2024)
5-26881486-T-C		not specified	Uncertain significance (Jan 03, 2024)
5-26881525-C-T		not specified	Uncertain significance (Apr 07, 2022)
5-26881527-T-C		not specified	Uncertain significance (Dec 21, 2022)
5-26881596-T-A		not specified	Uncertain significance (Mar 31, 2023)
5-26885667-C-A		not specified	Uncertain significance (Jun 06, 2023)
5-26885688-T-C			Benign (Mar 29, 2018)
5-26885779-T-C		not specified	Uncertain significance (Mar 23, 2022)
5-26885785-A-C		not specified	Uncertain significance (Mar 16, 2022)
5-26885796-G-A		not specified	Uncertain significance (Jul 12, 2023)
5-26885841-C-T		not specified	Uncertain significance (Sep 27, 2021)
5-26886040-C-T		not specified	Uncertain significance (Jan 29, 2024)
5-26889865-A-G		not specified	Uncertain significance (Apr 28, 2023)
5-26889890-C-T			Benign (May 16, 2018)
5-26889939-C-T		not specified	Uncertain significance (Dec 21, 2022)
5-26890442-G-T		not specified	Uncertain significance (Jan 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH9	protein_coding	protein_coding	ENST00000231021	11	240549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.831	0.169	125730	0	8	125738	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	345	450	0.767	0.0000246	5243
Missense in Polyphen		128	206.47	0.61993		2396
Synonymous	-2.81	209	163	1.28	0.00000961	1476
Loss of Function	4.29	6	32.3	0.186	0.00000168	402

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000446	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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.
• Pathway: Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.0943

Intolerance Scores

• loftool: 0.353
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.11

Haploinsufficiency Scores

• pHI: 0.425
• hipred: Y
• hipred_score: 0.778
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh9
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: cell morphogenesis;cell-cell junction assembly;homophilic cell adhesion via plasma membrane adhesion molecules;synapse assembly;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;adherens junction organization;cell-cell adhesion mediated by cadherin;cell-cell adhesion;synaptic membrane adhesion
• Cellular component: plasma membrane;cell-cell adherens junction;cell surface;catenin complex;integral component of postsynaptic membrane;integral component of presynaptic membrane
• Molecular function: molecular_function;calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding