CTNND1

catenin delta 1, the group of p120 catenin family|Armadillo repeat containing

Basic information

Region (hg38): 11:57753242-57819546

Previous symbols: [ "CTNND" ]

Links

ENSG00000198561 ∙ NCBI:1500 ∙ OMIM:601045 ∙ HGNC:2515 ∙ Uniprot:O60716 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• blepharocheilodontic syndrome 2 (Moderate), mode of inheritance: AD
• blepharocheilodontic syndrome (Supportive), mode of inheritance: AD
• blepharocheilodontic syndrome 2 (Strong), mode of inheritance: AD
• blepharocheilodontic syndrome 2 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blepharocheilodontic syndrome 2	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dermatologic; Dental	28301459

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTNND1 gene.

• not provided (54 variants)
• Inborn genetic diseases (48 variants)
• Blepharocheilodontic syndrome 2 (11 variants)
• Cleft lip with or without cleft palate (3 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTNND1 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				3	4	7
missense		1	72	5	3	81
nonsense	4	5				9
start loss						0
frameshift	2					2
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			2		6	8
Total	6	6	75	8	13

Variants in CTNND1

This is a list of pathogenic ClinVar variants found in the CTNND1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57791485-G-T			Uncertain significance (Nov 23, 2022)
11-57791500-T-G		Inborn genetic diseases	Uncertain significance (Oct 24, 2023)
11-57791506-G-C		Inborn genetic diseases	Uncertain significance (Mar 21, 2022)
11-57791507-C-T		Inborn genetic diseases	Uncertain significance (Mar 21, 2022)
11-57791520-C-T		CTNND1-related disorder	Likely benign (Mar 10, 2020)
11-57791533-C-G		Cleft lip with or without cleft palate	Uncertain significance (Nov 15, 2022)
11-57791594-C-T		Inborn genetic diseases	Uncertain significance (May 18, 2022)
11-57791626-G-C			Uncertain significance (Sep 04, 2019)
11-57791633-A-G			Likely benign (Nov 01, 2023)
11-57794013-G-C		Inborn genetic diseases	Uncertain significance (Apr 12, 2022)
11-57794014-G-A		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
11-57794016-C-T		CTNND1-related disorder • Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 05, 2022)
11-57794071-A-G		CTNND1-related disorder	Benign/Likely benign (Nov 01, 2023)
11-57795617-A-G		Inborn genetic diseases	Uncertain significance (May 31, 2022)
11-57795622-C-T			Uncertain significance (Oct 17, 2022)
11-57795631-A-T		CTNND1-related disorder	Likely benign (Jun 22, 2023)
11-57795632-T-C			Uncertain significance (Sep 20, 2021)
11-57795640-A-G		Inborn genetic diseases	Uncertain significance (May 22, 2023)
11-57795646-A-C		CTNND1-related disorder	Likely benign (Jan 20, 2023)
11-57795671-T-C		Inborn genetic diseases	Uncertain significance (May 31, 2023)
11-57795715-C-T		Inborn genetic diseases	Uncertain significance (Jan 27, 2022)
11-57795716-G-A		Inborn genetic diseases	Uncertain significance (Mar 06, 2023)
11-57795719-C-T			Uncertain significance (Nov 25, 2019)
11-57795728-C-T		Inborn genetic diseases	Uncertain significance (Nov 22, 2023)
11-57796457-G-A			Uncertain significance (Nov 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTNND1	protein_coding	protein_coding	ENST00000399050	19	66304

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000115	124648	0	8	124656	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	432	572	0.756	0.0000352	6260
Missense in Polyphen		141	215.27	0.65498		2269
Synonymous	2.19	160	199	0.803	0.0000105	1913
Loss of Function	6.00	4	49.6	0.0806	0.00000277	588

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000566	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000451	0.0000442
Middle Eastern	0.0000566	0.0000556
South Asian	0.0000354	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to and inhibits the transcriptional repressor ZBTB33, which may lead to activation of target genes of the Wnt signaling pathway (By similarity). Associates with and regulates the cell adhesion properties of both C-, E- and N-cadherins, being critical for their surface stability. Implicated both in cell transformation by SRC and in ligand-induced receptor signaling through the EGF, PDGF, CSF-1 and ERBB2 receptors. Promotes GLIS2 C-terminal cleavage. {ECO:0000250, ECO:0000269|PubMed:17344476, ECO:0000269|PubMed:20371349}.
• Disease: DISEASE: Blepharocheilodontic syndrome 2 (BCDS2) [MIM:617681]: A form of blepharocheilodontic syndrome, a rare autosomal dominant disorder. It is characterized by lower eyelid ectropion, upper eyelid distichiasis, euryblepharon, bilateral cleft lip and palate, and features of ectodermal dysplasia, including hair anomalies, conical teeth and tooth agenesis. An additional rare manifestation is imperforate anus. There is considerable phenotypic variability among affected individuals. {ECO:0000269|PubMed:28301459}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Adherens junction - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;Wnt Signaling Pathway and Pluripotency;Disease;Signal Transduction;VEGFA-VEGFR2 Pathway;Infectious disease;EGFR1;E-cadherin signaling in keratinocytes;Posttranslational regulation of adherens junction stability and dissassembly;Signaling by VEGF;Arf6 trafficking events;Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Signaling by Receptor Tyrosine Kinases;Cell-Cell communication;Stabilization and expansion of the E-cadherin adherens junction;N-cadherin signaling events;FGF signaling pathway;E-cadherin signaling in the nascent adherens junction;VEGFR2 mediated vascular permeability;InlA-mediated entry of Listeria monocytogenes into host cells;Listeria monocytogenes entry into host cells (Consensus)

Recessive Scores

• pRec: 0.272

Intolerance Scores

• loftool: 0.538
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.2

Haploinsufficiency Scores

• pHI: 0.749
• hipred: Y
• hipred_score: 0.800
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.664

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctnnd1
• Phenotype: cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; renal/urinary system phenotype; digestive/alimentary 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; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm

Zebrafish Information Network

• Gene name: ctnnd1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: cell-cell junction assembly;cell adhesion;brain development;Wnt signaling pathway;adherens junction organization;entry of bacterium into host cell;negative regulation of canonical Wnt signaling pathway;cell-cell adhesion;regulation of postsynaptic membrane neurotransmitter receptor levels
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane;cell-cell junction;cell-cell adherens junction;zonula adherens;catenin complex;lamellipodium;growth cone;midbody;dendritic spine;extracellular exosome;Schaffer collateral - CA1 synapse;hippocampal mossy fiber to CA3 synapse;presynaptic active zone cytoplasmic component;glutamatergic synapse;postsynaptic density, intracellular component
• Molecular function: signaling receptor binding;protein binding;protein kinase binding;cadherin binding