TBX20

T-box transcription factor 20, the group of T-box transcription factors

Basic information

Region (hg38): 7:35202430-35254100

Links

ENSG00000164532 ∙ NCBI:57057 ∙ OMIM:606061 ∙ HGNC:11598 ∙ Uniprot:Q9UMR3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• atrial septal defect 4 (Definitive), mode of inheritance: AD
• atrial septal defect 4 (Strong), mode of inheritance: AD
• atrial septal defect 4 (Strong), mode of inheritance: AD
• dilated cardiomyopathy (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Atrial septal defect 4	AD	Cardiovascular	Variants can result in a wide spectrum of cardiac-related disease, some of which may be challenging to recognize, and awareness may allow early medical and/or surgical management of manifestations, which can include valvular disease and cardiomyopathy in addition to frank structural anomalies such as ASD	Cardiovascular	17668378; 19762328

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBX20 gene.

• not provided (18 variants)
• Cardiovascular phenotype (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBX20 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			2	111	2	115
missense			255	3		258
nonsense	8	4	5			17
start loss						0
frameshift	11	2	6			19
inframe indel			9			9
splice donor/acceptor (+/-2bp)		5	1			6
splice region			10	18		28
non coding			4	42	17	63
Total	19	11	282	156	19

Highest pathogenic variant AF is 0.00000657

Variants in TBX20

This is a list of pathogenic ClinVar variants found in the TBX20 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-35202440-G-A		Cardiovascular phenotype • TBX20-related disorder	Uncertain significance (Aug 15, 2023)
7-35202442-C-G			Likely benign (Apr 24, 2022)
7-35202442-C-T		Cardiovascular phenotype	Likely benign (Jul 28, 2023)
7-35202443-G-A		Cardiovascular phenotype	Conflicting classifications of pathogenicity (Nov 07, 2023)
7-35202445-C-T		Cardiovascular phenotype	Uncertain significance (Oct 19, 2023)
7-35202452-G-A			Uncertain significance (Nov 28, 2023)
7-35202453-C-G			Uncertain significance (Mar 19, 2023)
7-35202453-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
7-35202455-G-T			Uncertain significance (Oct 25, 2022)
7-35202462-G-A			Uncertain significance (Jan 21, 2022)
7-35202464-C-A		Cardiovascular phenotype	Conflicting classifications of pathogenicity (Jun 13, 2023)
7-35202464-C-T		Cardiovascular phenotype • Atrial septal defect 4	Uncertain significance (May 31, 2024)
7-35202465-G-A		Cardiovascular phenotype • Atrial septal defect 4	Uncertain significance (Jun 18, 2024)
7-35202466-T-C		Cardiovascular phenotype	Likely benign (Jan 31, 2024)
7-35202471-C-T		Cardiovascular phenotype	Uncertain significance (Aug 24, 2023)
7-35202472-T-C		Cardiovascular phenotype	Likely benign (Jan 22, 2024)
7-35202477-T-C		Cardiovascular phenotype	Uncertain significance (Apr 09, 2023)
7-35202481-A-G		Cardiovascular phenotype	Likely benign (Nov 19, 2022)
7-35202489-G-T		TBX20-related disorder	Uncertain significance (May 08, 2023)
7-35202490-C-T			Likely benign (Dec 09, 2022)
7-35202492-C-G			Uncertain significance (Jul 12, 2023)
7-35202502-A-G			Likely benign (Sep 29, 2021)
7-35202505-G-C		Cardiovascular phenotype	Uncertain significance (Jan 26, 2022)
7-35202510-G-T		Cardiovascular phenotype	Uncertain significance (Oct 30, 2022)
7-35202515-C-T		Cardiovascular phenotype	Uncertain significance (Oct 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBX20	protein_coding	protein_coding	ENST00000408931	8	51717

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.973	0.0270	125739	0	4	125743	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.68	176	251	0.701	0.0000125	2908
Missense in Polyphen		44	85.7	0.51342		989
Synonymous	-0.604	109	101	1.08	0.00000512	908
Loss of Function	3.72	2	20.0	0.100	0.00000109	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional activator and repressor required for cardiac development and may have key roles in the maintenance of functional and structural phenotypes in adult heart. {ECO:0000250}.
• Disease: DISEASE: Atrial septal defect 4 (ASD4) [MIM:611363]: A congenital heart malformation characterized by incomplete closure of the wall between the atria resulting in blood flow from the left to the right atria. Patients show other heart abnormalities including defects in septation, chamber growth and valvulogenesis. The disease is not associated with defects in the cardiac conduction system or with non-cardiac abnormalities. {ECO:0000269|PubMed:17668378, ECO:0000269|PubMed:19762328}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Heart Development;Cardiac Progenitor Differentiation (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.130
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.695
• hipred: Y
• hipred_score: 0.837
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbx20
• Phenotype: 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); normal 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); embryo phenotype; homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: tbx20
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;branching involved in blood vessel morphogenesis;endoderm formation;neuron migration;heart looping;embryonic heart tube morphogenesis;outflow tract septum morphogenesis;tricuspid valve development;aortic valve morphogenesis;pulmonary valve formation;endocardial cushion morphogenesis;cardiac chamber formation;cardiac right ventricle morphogenesis;endocardial cushion formation;cardiac septum development;pericardium morphogenesis;muscle contraction;blood circulation;cell population proliferation;dorsal/ventral pattern formation;negative regulation of SMAD protein complex assembly;visceral motor neuron differentiation;foramen ovale closure;embryonic heart tube elongation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;lateral mesoderm formation;cardiac muscle tissue morphogenesis;positive regulation of cardiac muscle cell proliferation;atrial septum morphogenesis;pulmonary vein morphogenesis
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;RNA polymerase II activating transcription factor binding;DNA-binding transcription activator activity, RNA polymerase II-specific