TEAD1

TEA domain transcription factor 1, the group of TEA domain transcription factors

Basic information

Region (hg38): 11:12674420-12944737

Previous symbols: [ "TCF13", "AA" ]

Links

ENSG00000187079 ∙ NCBI:7003 ∙ OMIM:189967 ∙ HGNC:11714 ∙ Uniprot:P28347 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• helicoid peripapillary chorioretinal degeneration (Supportive), mode of inheritance: AD
• helicoid peripapillary chorioretinal degeneration (Strong), mode of inheritance: AD
• Aicardi syndrome (Limited), mode of inheritance: AD
• helicoid peripapillary chorioretinal degeneration (Limited), mode of inheritance: AD
• helicoid peripapillary chorioretinal degeneration (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Sveinsson choreoretinal atrophy	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	Ophthalmologic	15016762

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TEAD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEAD1 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				58	2	60
missense			106	2		108
nonsense			1			1
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			7	11	2	20
non coding				32	6	38
Total	0	0	108	92	8

Variants in TEAD1

This is a list of pathogenic ClinVar variants found in the TEAD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-12764253-C-T			Likely benign (Oct 28, 2023)
11-12764254-G-C			Uncertain significance (Mar 22, 2023)
11-12764264-G-A			Uncertain significance (Jul 19, 2022)
11-12764271-C-T			Benign (Nov 27, 2023)
11-12764273-A-G			Uncertain significance (Nov 30, 2021)
11-12764285-G-A		Inborn genetic diseases	Uncertain significance (Sep 20, 2023)
11-12764300-C-T			Uncertain significance (Dec 30, 2019)
11-12764308-C-T			Uncertain significance (Oct 24, 2022)
11-12764309-C-A		Inborn genetic diseases	Uncertain significance (Nov 28, 2023)
11-12764311-A-G			Uncertain significance (Oct 14, 2021)
11-12764313-T-A			Likely benign (Dec 09, 2023)
11-12764331-G-A			Likely benign (Jan 19, 2024)
11-12764331-G-C			Likely benign (Jan 15, 2024)
11-12764343-C-T			Likely benign (Aug 23, 2022)
11-12764345-A-C			Uncertain significance (Nov 14, 2020)
11-12764349-C-T			Likely benign (Sep 27, 2022)
11-12764361-T-C			Likely benign (Dec 22, 2023)
11-12764367-G-A			Likely benign (Oct 30, 2020)
11-12764369-C-A			Uncertain significance (Apr 11, 2022)
11-12764388-A-T			Likely benign (Jun 27, 2022)
11-12764389-T-C			Uncertain significance (Oct 14, 2023)
11-12764408-T-C			Uncertain significance (Sep 22, 2022)
11-12764418-C-T			Benign (Nov 13, 2023)
11-12862240-T-C			Likely benign (Aug 24, 2022)
11-12862299-G-A			Likely benign (Jan 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEAD1	protein_coding	protein_coding	ENST00000361985	11	270330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000199	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	166	238	0.698	0.0000135	2835
Missense in Polyphen		24	66.389	0.3615		862
Synonymous	-0.366	92	87.6	1.05	0.00000542	779
Loss of Function	4.57	0	24.3	0.00	0.00000133	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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 cooperatively to the SPH and GT-IIC 'enhansons' (5'-GTGGAATGT-3') and activates transcription in vivo in a cell-specific manner. The activation function appears to be mediated by a limiting cell-specific transcriptional intermediary factor (TIF). Involved in cardiac 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: 0.413

Intolerance Scores

• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.799
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tead1
• 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); hearing/vestibular/ear phenotype; vision/eye phenotype; skeleton 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; 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); muscle phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: transcription initiation from RNA polymerase II promoter;hippo signaling;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;protein-containing complex assembly;positive regulation of pri-miRNA transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;transcription factor complex;TEAD-1-YAP complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;RNA polymerase II transcription factor binding;transcription regulator recruiting activity;transcription coactivator binding;DNA binding;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding;transcription regulatory region DNA binding;protein heterodimerization activity