TEAD2

TEA domain transcription factor 2, the group of TEA domain transcription factors

Basic information

Region (hg38): 19:49340595-49362457

Links

ENSG00000074219 ∙ NCBI:8463 ∙ OMIM:601729 ∙ HGNC:11715 ∙ Uniprot:Q15562 ∙ 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 TEAD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEAD2 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						0
missense			18		3	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	3

Variants in TEAD2

This is a list of pathogenic ClinVar variants found in the TEAD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49342464-C-T		not specified	Uncertain significance (Jul 25, 2023)
19-49342506-G-T		not specified	Uncertain significance (Dec 13, 2023)
19-49342527-C-T		not specified	Uncertain significance (Apr 27, 2024)
19-49343374-C-T		not specified	Uncertain significance (Nov 08, 2022)
19-49347227-C-T		not specified	Uncertain significance (Oct 13, 2023)
19-49348705-A-T		not specified	Uncertain significance (Mar 18, 2024)
19-49348722-G-A		not specified	Uncertain significance (Aug 23, 2021)
19-49348773-C-G			Benign (Dec 31, 2019)
19-49348776-C-T		not specified	Uncertain significance (Jan 31, 2024)
19-49348797-G-A		not specified	Uncertain significance (Jun 21, 2022)
19-49348804-T-G		not specified	Uncertain significance (Sep 14, 2022)
19-49348813-G-A			Benign (Dec 31, 2019)
19-49348840-C-T		not specified	Uncertain significance (Aug 16, 2022)
19-49351321-G-A		not specified	Uncertain significance (Apr 25, 2022)
19-49351363-A-G		not specified	Uncertain significance (Oct 03, 2022)
19-49355359-T-C		not specified	Uncertain significance (Feb 22, 2023)
19-49357264-C-A			Benign (Jul 15, 2018)
19-49357286-C-G		not specified	Uncertain significance (Dec 08, 2023)
19-49359851-C-G		not specified	Uncertain significance (Apr 08, 2024)
19-49359939-C-T		not specified	Uncertain significance (Feb 11, 2022)
19-49359967-C-T		not specified	Uncertain significance (Oct 12, 2021)
19-49360026-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-49360050-G-A		not specified	Uncertain significance (Dec 06, 2021)
19-49360063-G-A		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEAD2	protein_coding	protein_coding	ENST00000598810	12	21863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000152	0.992	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.858	244	285	0.857	0.0000179	2898
Missense in Polyphen		84	104.45	0.80423		1083
Synonymous	-0.115	123	121	1.01	0.00000824	919
Loss of Function	2.38	14	27.5	0.509	0.00000158	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000181
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.000263	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor which plays a key role in the Hippo signaling pathway, a pathway involved in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein MST1/MST2, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. Acts by mediating gene expression of YAP1 and WWTR1/TAZ, thereby regulating cell proliferation, migration and epithelial mesenchymal transition (EMT) induction. Binds to the SPH and GT-IIC 'enhansons' (5'- GTGGAATGT-3'). May be involved in the gene regulation of neural development. Binds to the M-CAT motif. {ECO:0000269|PubMed:18579750, ECO:0000269|PubMed:19324877}.
• Pathway: Hippo signaling pathway - Homo sapiens (human);Hippo signaling pathway - multiple species - Homo sapiens (human);Mesodermal Commitment Pathway;miR-509-3p alteration of YAP1-ECM axis;Gene expression (Transcription);RUNX3 regulates YAP1-mediated transcription;Transcriptional regulation by RUNX3;Generic Transcription Pathway;RNA Polymerase II Transcription;YAP1- and WWTR1 (TAZ)-stimulated gene expression (Consensus)

Recessive Scores

• pRec: 0.381

Intolerance Scores

• loftool: 0.679
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.61

Haploinsufficiency Scores

• pHI: 0.606
• hipred: Y
• hipred_score: 0.782
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.954

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tead2
• Phenotype: growth/size/body region phenotype; cellular 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); 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; skeleton phenotype

Gene ontology

• Biological process: vasculogenesis;neural tube closure;embryonic heart tube morphogenesis;regulation of transcription, DNA-templated;transcription initiation from RNA polymerase II promoter;notochord development;hippo signaling;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;paraxial mesoderm development;lateral mesoderm development;negative regulation of cell death;protein-containing complex assembly;cellular response to retinoic acid;regulation of stem cell differentiation
• Cellular component: nucleus;nucleoplasm;transcription factor complex;cytosol;intracellular membrane-bounded organelle;TEAD-2-YAP complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;transcription regulator recruiting activity;transcription coactivator binding;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding;transcription regulatory region DNA binding;protein heterodimerization activity;disordered domain specific binding