TFF3

trefoil factor 3

Basic information

Region (hg38): 21:42311666-42315409

Links

ENSG00000160180 ∙ NCBI:7033 ∙ OMIM:600633 ∙ HGNC:11757 ∙ Uniprot:Q07654 ∙ 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 TFF3 gene.

• Inborn genetic diseases (2 variants)
• not provided (1 variants)

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			1		1	2
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	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: gnomAD

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: dbNSFP

• 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
• 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