CTNNA3

catenin alpha 3, the group of Alpha catenins|MicroRNA protein coding host genes

Basic information

Region (hg38): 10:65912456-67763637

Links

ENSG00000183230 ∙ NCBI:29119 ∙ OMIM:607667 ∙ HGNC:2511 ∙ Uniprot:Q9UI47 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• arrhythmogenic right ventricular dysplasia 13 (Limited), mode of inheritance: AD
• arrhythmogenic right ventricular dysplasia 13 (Limited), mode of inheritance: AD
• arrhythmogenic right ventricular cardiomyopathy (Limited), mode of inheritance: AD
• congenital heart disease (Disputed Evidence), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Arrhythmogenic right ventricular dysplasia, familial, 13	AD	Cardiovascular	Individuals have been described as presenting with arrhthymias and echocardiographic findings including right ventricular dilatation and dyskinesia, and awareness can allow surveillance (eg, with echocardiogram, electrocardiogram) and preventive measures and early treatment (eg ,with ICD)	Cardiovascular	23136403

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTNNA3 gene.

• Arrhythmogenic right ventricular dysplasia 13 (569 variants)
• Inborn genetic diseases (278 variants)
• not provided (156 variants)
• not specified (41 variants)
• CTNNA3-related condition (4 variants)
• Primary familial hypertrophic cardiomyopathy (3 variants)
• Primary dilated cardiomyopathy (3 variants)
• Long QT syndrome (2 variants)
• Left ventricular noncompaction cardiomyopathy (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTNNA3 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				173	3	176
missense			365	16	5	386
nonsense			12			12
start loss			1			1
frameshift		1	17			18
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1	11			12
splice region			17	12	1	30
non coding			16	61	69	146
Total	0	2	423	250	77

Variants in CTNNA3

This is a list of pathogenic ClinVar variants found in the CTNNA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-65920087-C-T			Benign (Sep 11, 2018)
10-65920330-T-C		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Nov 22, 2022)
10-65920332-A-G		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Mar 14, 2020)
10-65920334-T-C		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Feb 21, 2022)
10-65920341-G-T		Arrhythmogenic right ventricular dysplasia 13 • not specified	Uncertain significance (Jul 11, 2022)
10-65920348-T-C		Arrhythmogenic right ventricular dysplasia 13	Likely benign (Dec 13, 2018)
10-65920349-C-T		not specified	Uncertain significance (Jul 11, 2022)
10-65920353-A-G		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Sep 17, 2023)
10-65920364-A-G		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Apr 21, 2022)
10-65920368-G-T		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Oct 25, 2022)
10-65920370-A-C		not specified	Uncertain significance (Dec 18, 2022)
10-65920371-A-G		Arrhythmogenic right ventricular dysplasia 13	Likely benign (Jan 22, 2024)
10-65920376-T-C		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Dec 29, 2022)
10-65920379-A-AT		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Jan 04, 2024)
10-65920383-T-G		not specified	Uncertain significance (Oct 11, 2021)
10-65920388-T-G		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Sep 22, 2017)
10-65920389-T-G		not specified	Uncertain significance (Aug 13, 2023)
10-65920390-T-C		Arrhythmogenic right ventricular dysplasia 13 • not specified	Likely benign (Jun 09, 2021)
10-65920395-A-G		not specified	Uncertain significance (Jun 14, 2023)
10-65920400-C-T		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Nov 25, 2023)
10-65920401-G-A		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Feb 04, 2023)
10-65920401-G-T		Arrhythmogenic right ventricular dysplasia 13	Likely benign (Oct 03, 2021)
10-65920402-T-G		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (Jan 14, 2022)
10-65920404-T-G		Arrhythmogenic right ventricular dysplasia 13	Likely benign (Dec 27, 2019)
10-65920417-C-T		Arrhythmogenic right ventricular dysplasia 13 • not specified	Benign/Likely benign (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTNNA3	protein_coding	protein_coding	ENST00000433211	17	1783652

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.02e-12	0.973	125595	0	153	125748	0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.11	565	495	1.14	0.0000263	5884
Missense in Polyphen		13	26.369	0.49301		324
Synonymous	-0.516	184	175	1.05	0.00000941	1703
Loss of Function	2.34	26	42.4	0.613	0.00000225	535

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000861	0.000858
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000655	0.000653
Finnish	0.00111	0.00111
European (Non-Finnish)	0.000477	0.000475
Middle Eastern	0.000655	0.000653
South Asian	0.00118	0.00105
Other	0.000985	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in formation of stretch-resistant cell- cell adhesion complexes. {ECO:0000303|PubMed:11590244}.
• Pathway: Gastric cancer - Homo sapiens (human);Adherens junction - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Arrhythmogenic Right Ventricular Cardiomyopathy;Endometrial cancer (Consensus)

Recessive Scores

• pRec: 0.186

Intolerance Scores

• loftool: 0.863
• rvis_EVS: -1.01
• rvis_percentile_EVS: 8.2

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.469
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.619

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctnna3
• 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); muscle phenotype

Gene ontology

• Biological process: bundle of His cell-Purkinje myocyte adhesion involved in cell communication;regulation of heart rate by cardiac conduction;cell-cell adhesion;regulation of ventricular cardiac muscle cell action potential
• Cellular component: cytoplasm;cytoskeleton;fascia adherens;lamellipodium
• Molecular function: protein binding;beta-catenin binding;cadherin binding;actin filament binding