TGFA
transforming growth factor alpha
Basic information
Region (hg38): 2:70447284-70554193
Links
Phenotypes
GenCC
Source:
- tooth agenesis (Supportive), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| missense | 11 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 2 | |||||
| Total | 0 | 0 | 9 | 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) | ||
| 2-70453260-C-T | not specified | Uncertain significance (May 02, 2024) | ||
| 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) | ||
| 2-70465718-G-T | not specified | Uncertain significance (May 20, 2024) | ||
| 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:
| 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:
- 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