TGFA

transforming growth factor alpha

Basic information

Region (hg38): 2:70447283-70554193

Links

ENSG00000163235 ∙ NCBI:7039 ∙ OMIM:190170 ∙ HGNC:11765 ∙ Uniprot:P01135 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• tooth agenesis (Supportive), mode of inheritance: AD

ClinVar

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

• Inborn genetic diseases (7 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TGFA 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	2
missense			6	1	1	8
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	6	3	3

Variants in TGFA

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

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

Position	Type	Phenotype	Significance	ClinVar
2-70450875-A-G			Likely benign (Aug 17, 2018)
2-70453221-T-G		not specified	Uncertain significance (Apr 13, 2022)
2-70453238-G-T		not specified	Uncertain significance (Apr 17, 2023)
2-70453253-A-T		not specified	Uncertain significance (Apr 13, 2022)
2-70453272-C-T		not specified	Uncertain significance (Apr 14, 2023)
2-70453287-G-A		not specified	Uncertain significance (Sep 20, 2023)
2-70456379-C-T			Benign (Aug 20, 2018)
2-70456400-C-T		not specified	Uncertain significance (Mar 24, 2023)
2-70456428-A-G			Benign (Aug 17, 2018)
2-70456472-C-T		not specified	Uncertain significance (Nov 10, 2022)
2-70465606-G-A			Likely benign (Jun 15, 2018)
2-70465703-T-C		not specified	Uncertain significance (Sep 22, 2023)
2-70514867-G-A		not specified	Likely benign (Jun 11, 2021)
2-70514890-C-T			Benign (Nov 20, 2018)
2-70514916-T-C			Benign (Nov 20, 2018)
2-70553757-G-A		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TGFA	protein_coding	protein_coding	ENST00000295400	6	106914

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.720	0.277	125723	0	6	125729	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.758	72	92.5	0.778	0.00000532	1010
Missense in Polyphen		19	27.924	0.68042		334
Synonymous	1.00	34	42.3	0.804	0.00000289	320
Loss of Function	2.39	1	8.51	0.118	4.49e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: TGF alpha is a mitogenic polypeptide that is able to bind to the EGF receptor/EGFR and to act synergistically with TGF beta to promote anchorage-independent cell proliferation in soft agar.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Non-small cell lung cancer - Homo sapiens (human);Renal cell carcinoma - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Glioma - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);EGFR Inhibitor Pathway, Pharmacodynamics;EGF-Core;Integrated Lung Cancer Pathway;Extracellular vesicle-mediated signaling in recipient cells;Nuclear Receptors Meta-Pathway;NRF2 pathway;Photodynamic therapy-induced HIF-1 survival signaling;Lung fibrosis;Association Between Physico-Chemical Features and Toxicity Associated Pathways;BMP Signaling Pathway in Eyelid Development;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors;PI3K-Akt Signaling Pathway;Type 2 papillary renal cell carcinoma;ErbB Signaling Pathway;Signal Transduction;Gene expression (Transcription);Vesicle-mediated transport;Membrane Trafficking;Generic Transcription Pathway;Post-translational protein modification;Metabolism of proteins;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;RNA Polymerase II Transcription;GPCR signaling-G alpha s Epac and ERK;Cargo concentration in the ER;GPCR signaling-G alpha s PKA and ERK;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Signaling by Nuclear Receptors;Direct p53 effectors;TFAP2 (AP-2) family regulates transcription of growth factors and their receptors;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors;Estrogen-dependent gene expression;GPCR signaling-G alpha i;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;ESR-mediated signaling;FOXM1 transcription factor network;ErbB receptor signaling network (Consensus)

Recessive Scores

• pRec: 0.750

Intolerance Scores

• loftool: 0.599
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.529
• hipred: Y
• hipred_score: 0.687
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.959

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tgfa
• 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); reproductive system phenotype; digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype; skeleton phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands 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); endocrine/exocrine gland phenotype; muscle phenotype; craniofacial phenotype

Gene ontology

• Biological process: activation of MAPK activity;regulation of transcription by RNA polymerase II;endoplasmic reticulum to Golgi vesicle-mediated transport;epidermal growth factor receptor signaling pathway;cell population proliferation;positive regulation of cell population proliferation;positive regulation of epidermal growth factor-activated receptor activity;positive regulation of mitotic nuclear division;COPII vesicle coating;positive regulation of epithelial cell proliferation;positive regulation of cell division
• Cellular component: Golgi membrane;extracellular space;endoplasmic reticulum membrane;plasma membrane;cell surface;ER to Golgi transport vesicle membrane;integral component of membrane;basolateral plasma membrane;cytoplasmic vesicle;endoplasmic reticulum-Golgi intermediate compartment membrane;perinuclear region of cytoplasm
• Molecular function: epidermal growth factor receptor binding;protein binding;growth factor activity