TFF3
Basic information
Region (hg38): 21:42311667-42315409
Links
Phenotypes
GenCC
Source:
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 TFF3 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 1 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 1 |
Variants in TFF3
This is a list of pathogenic ClinVar variants found in the TFF3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 21-42313518-C-T | Benign (Jul 25, 2018) | |||
| 21-42315302-C-T | not specified | Uncertain significance (Feb 17, 2024) | ||
| 21-42315356-A-G | not specified | Uncertain significance (Dec 27, 2023) | ||
| 21-42315361-G-A | not specified | Uncertain significance (May 23, 2023) | ||
| 21-42315373-A-G | not specified | Uncertain significance (Apr 22, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TFF3 | protein_coding | protein_coding | ENST00000518498 | 3 | 3985 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0159 | 0.716 | 123210 | 0 | 1 | 123211 | 0.00000406 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.514 | 44 | 54.7 | 0.804 | 0.00000300 | 599 |
| Missense in Polyphen | 14 | 18.074 | 0.77458 | 198 | ||
| Synonymous | -0.0958 | 26 | 25.4 | 1.02 | 0.00000159 | 193 |
| Loss of Function | 0.691 | 3 | 4.60 | 0.652 | 2.80e-7 | 46 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000300 | 0.0000300 |
| 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:
- Function
- FUNCTION: Involved in the maintenance and repair of the intestinal mucosa. Promotes the mobility of epithelial cells in healing processes (motogen). {ECO:0000269|PubMed:11694446}.;
- Pathway
- Signal Transduction;trefoil factors initiate mucosal healing;Signaling by Nuclear Receptors;Estrogen-dependent gene expression;ESR-mediated signaling;HIF-1-alpha transcription factor network;IL4-mediated signaling events
(Consensus)
Intolerance Scores
- loftool
- 0.684
- rvis_EVS
- 0.39
- rvis_percentile_EVS
- 75.87
Haploinsufficiency Scores
- pHI
- 0.163
- hipred
- N
- hipred_score
- 0.123
- ghis
- 0.418
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.00288
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tff3
- Phenotype
- homeostasis/metabolism phenotype; immune system phenotype; digestive/alimentary phenotype;
Gene ontology
- Biological process
- regulation of glucose metabolic process;maintenance of gastrointestinal epithelium
- Cellular component
- extracellular region;extracellular space;secretory granule
- Molecular function
- molecular_function;protein binding