TFF1
Basic information
Region (hg38): 21:42362282-42366535
Previous symbols: [ "BCEI" ]
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 TFF1 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 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 6 | 0 | 2 |
Variants in TFF1
This is a list of pathogenic ClinVar variants found in the TFF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 21-42362504-G-A | Benign (Jul 26, 2018) | |||
| 21-42363272-A-T | not specified | Uncertain significance (Aug 08, 2022) | ||
| 21-42363278-T-C | not specified | Uncertain significance (Feb 23, 2025) | ||
| 21-42363281-G-T | not specified | Uncertain significance (Nov 13, 2023) | ||
| 21-42363305-C-A | not specified | Uncertain significance (Mar 14, 2023) | ||
| 21-42363399-T-C | not specified | Uncertain significance (Feb 27, 2023) | ||
| 21-42366424-G-A | Benign (Aug 01, 2018) | |||
| 21-42366445-C-T | not specified | Uncertain significance (Feb 18, 2025) | ||
| 21-42366447-T-A | not specified | Uncertain significance (Dec 21, 2022) | ||
| 21-42366450-A-T | not specified | Uncertain significance (Jul 27, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TFF1 | protein_coding | protein_coding | ENST00000291527 | 3 | 4313 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000889 | 0.360 | 125731 | 0 | 12 | 125743 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.134 | 57 | 54.2 | 1.05 | 0.00000342 | 541 |
| Missense in Polyphen | 14 | 15.352 | 0.9119 | 170 | ||
| Synonymous | -0.243 | 25 | 23.5 | 1.06 | 0.00000174 | 166 |
| Loss of Function | -0.453 | 4 | 3.13 | 1.28 | 1.33e-7 | 38 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000235 | 0.000235 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Stabilizer of the mucous gel overlying the gastrointestinal mucosa that provides a physical barrier against various noxious agents. May inhibit the growth of calcium oxalate crystals in urine. {ECO:0000269|PubMed:16308573}.;
- Pathway
- Estrogen signaling pathway - Homo sapiens (human);Signal Transduction;trefoil factors initiate mucosal healing;FOXA1 transcription factor network;Signaling by Nuclear Receptors;Estrogen-dependent gene expression;ESR-mediated signaling;Validated nuclear estrogen receptor alpha network
(Consensus)
Recessive Scores
- pRec
- 0.255
Intolerance Scores
- loftool
- 0.685
- rvis_EVS
- 0.53
- rvis_percentile_EVS
- 80.58
Haploinsufficiency Scores
- pHI
- 0.130
- hipred
- N
- hipred_score
- 0.276
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.688
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tff1
- Phenotype
- neoplasm; digestive/alimentary phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- carbohydrate metabolic process;negative regulation of cell population proliferation;response to iron ion;regulation of signaling receptor activity;cell differentiation;maintenance of gastrointestinal epithelium;response to immobilization stress;response to peptide hormone
- Cellular component
- extracellular region;extracellular space
- Molecular function
- protein binding;growth factor activity