TFF2

trefoil factor 2

Basic information

Region (hg38): 21:42346357-42350997

Previous symbols: [ "SML1" ]

Links

ENSG00000160181 ∙ NCBI:7032 ∙ OMIM:182590 ∙ HGNC:11756 ∙ Uniprot:Q03403 ∙ 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 TFF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFF2 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	1
missense			6	2	1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	2	2

Variants in TFF2

This is a list of pathogenic ClinVar variants found in the TFF2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
21-42347493-A-G			Benign (Dec 31, 2019)
21-42347551-C-T		not specified	Uncertain significance (Jul 30, 2023)
21-42347596-C-T		not specified	Likely benign (Sep 22, 2023)
21-42347612-C-G		not specified	Uncertain significance (Oct 14, 2021)
21-42347629-G-A		not specified	Uncertain significance (Feb 17, 2024)
21-42349974-C-T		not specified	Uncertain significance (Jun 07, 2024)
21-42349977-G-A		not specified	Uncertain significance (Mar 30, 2024)
21-42349980-A-T		not specified	Uncertain significance (Mar 19, 2024)
21-42350007-T-C		not specified	Uncertain significance (Jan 27, 2022)
21-42350890-C-T		not specified	Uncertain significance (Jun 07, 2024)
21-42350918-C-T		not specified	Uncertain significance (Jan 24, 2024)
21-42350926-G-A		not specified	Likely benign (Apr 27, 2023)
21-42350945-C-T		not specified	Uncertain significance (Jan 22, 2024)
21-42350951-G-A			Benign (Jul 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFF2	protein_coding	protein_coding	ENST00000291526	4	4772

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.22e-7	0.0835	125728	0	17	125745	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.460	67	78.5	0.854	0.00000479	829
Missense in Polyphen		27	32.333	0.83507		355
Synonymous	0.344	32	34.6	0.926	0.00000241	239
Loss of Function	-0.737	9	6.91	1.30	3.78e-7	72

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000247	0.000217
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000561	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000219	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits gastrointestinal motility and gastric acid secretion. Could function as a structural component of gastric mucus, possibly by stabilizing glycoproteins in the mucus gel through interactions with carbohydrate side chains (By similarity). {ECO:0000250}.
• Pathway: trefoil factors initiate mucosal healing (Consensus)

Recessive Scores

• pRec: 0.215

Intolerance Scores

• loftool: 0.694
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.22

Haploinsufficiency Scores

• pHI: 0.0909
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tff2
• Phenotype: immune system phenotype; digestive/alimentary phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: maintenance of gastrointestinal epithelium;negative regulation of gastric acid secretion;chemokine-mediated signaling pathway
• Cellular component: extracellular space
• Molecular function: protein binding;CXCR4 chemokine receptor binding