TEAD4

TEA domain transcription factor 4, the group of TEA domain transcription factors

Basic information

Region (hg38): 12:2959329-3040676

Previous symbols: [ "TCF13L1" ]

Links

ENSG00000197905 ∙ NCBI:7004 ∙ OMIM:601714 ∙ HGNC:11717 ∙ Uniprot:Q15561 ∙ 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 TEAD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEAD4 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
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			2			2
Total	0	0	23	2	0

Variants in TEAD4

This is a list of pathogenic ClinVar variants found in the TEAD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-2994819-C-T		not specified	Uncertain significance (Nov 05, 2021)
12-2994854-G-T		not specified	Uncertain significance (Feb 15, 2023)
12-2994897-G-A		not specified	Uncertain significance (Apr 06, 2022)
12-2994932-G-A		not specified	Uncertain significance (Aug 10, 2021)
12-2994972-C-T		not specified	Uncertain significance (May 17, 2023)
12-3011006-C-T		not specified	Uncertain significance (Apr 21, 2022)
12-3011024-C-T		not specified	Uncertain significance (Dec 28, 2022)
12-3012210-G-C		not specified	Uncertain significance (Nov 27, 2023)
12-3017398-G-C		not specified	Uncertain significance (Mar 01, 2023)
12-3017497-C-T		not specified	Uncertain significance (Aug 17, 2021)
12-3017506-G-A		not specified	Uncertain significance (Jan 31, 2024)
12-3017510-G-A		not specified	Uncertain significance (Oct 27, 2022)
12-3019115-T-C		not specified	Likely benign (Apr 08, 2024)
12-3019147-T-C		not specified	Uncertain significance (Apr 17, 2023)
12-3020630-G-T			Likely benign (Aug 01, 2022)
12-3020652-G-T		not specified	Uncertain significance (Jun 03, 2022)
12-3020657-G-A		not specified	Likely benign (Oct 13, 2021)
12-3020675-C-T		not specified	Uncertain significance (Jun 07, 2024)
12-3020693-C-G		not specified	Uncertain significance (Dec 12, 2023)
12-3020705-G-A		not specified	Uncertain significance (Jun 16, 2022)
12-3020768-G-A		not specified	Uncertain significance (Dec 18, 2023)
12-3021862-G-A		not specified	Uncertain significance (Jan 19, 2024)
12-3021910-G-T		not specified	Uncertain significance (May 30, 2024)
12-3021923-G-T		not specified	Uncertain significance (Jan 30, 2024)
12-3021980-G-A		not specified	Uncertain significance (Apr 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEAD4	protein_coding	protein_coding	ENST00000359864	11	81344

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000323	0.988	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	216	281	0.768	0.0000179	2850
Missense in Polyphen		74	113.22	0.65361		1190
Synonymous	-0.231	122	119	1.03	0.00000837	831
Loss of Function	2.24	11	22.4	0.490	9.56e-7	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000534	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000329	0.0000327
Other	0.00	0.00

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 specifically and non-cooperatively to the Sph and GT-IIC 'enhansons' (5'-GTGGAATGT-3') and activates transcription. 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);Preimplantation Embryo;VEGFA-VEGFR2 Signaling 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: 0.141

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.58

Haploinsufficiency Scores

• pHI: 0.928
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tead4
• Phenotype: embryo 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); normal phenotype

Gene ontology

• Biological process: skeletal system development;regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;muscle organ development;hippo signaling;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding;transcription regulatory region DNA binding