TFF1

trefoil factor 1

Basic information

Region (hg38): 21:42362282-42366535

Previous symbols: [ "BCEI" ]

Links

ENSG00000160182

∙ NCBI:7031 ∙ OMIM:113710 ∙ HGNC:11755 ∙ Uniprot:P04155 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TFF1 gene.

not_specified (9 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_000003225.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			9 clinvar			9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	9	0	1

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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