TCF7
transcription factor 7, the group of TCF/LEF transcription factor family|Wnt enhanceosome complex
Basic information
Region (hg38): 5:134114681-134151865
Links
Phenotypes
GenCC
Source:
No genCC data.
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 TCF7 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 | 3 | |||||
| missense | 31 | 31 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 31 | 3 | 0 |
Variants in TCF7
This is a list of pathogenic ClinVar variants found in the TCF7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-134114920-A-G | not specified | Uncertain significance (Dec 17, 2021) | ||
| 5-134114943-G-C | not specified | Uncertain significance (May 04, 2022) | ||
| 5-134114964-C-T | not specified | Uncertain significance (Jul 14, 2022) | ||
| 5-134114988-G-A | not specified | Uncertain significance (Apr 15, 2024) | ||
| 5-134115031-C-T | not specified | Uncertain significance (Apr 07, 2023) | ||
| 5-134115118-T-G | not specified | Uncertain significance (Nov 09, 2021) | ||
| 5-134115121-C-T | not specified | Uncertain significance (Jan 20, 2023) | ||
| 5-134115123-G-A | not specified | Uncertain significance (Mar 14, 2023) | ||
| 5-134115126-G-A | not specified | Uncertain significance (Aug 16, 2022) | ||
| 5-134115129-G-T | not specified | Uncertain significance (Sep 03, 2024) | ||
| 5-134115135-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
| 5-134115138-G-A | not specified | Uncertain significance (Apr 07, 2022) | ||
| 5-134115370-C-A | not specified | Uncertain significance (Mar 24, 2023) | ||
| 5-134115370-C-T | not specified | Uncertain significance (Nov 13, 2024) | ||
| 5-134115385-A-G | not specified | Uncertain significance (Jul 10, 2024) | ||
| 5-134115917-G-T | not specified | Uncertain significance (Aug 27, 2024) | ||
| 5-134115923-G-C | not specified | Uncertain significance (Jan 24, 2023) | ||
| 5-134115924-A-C | not specified | Uncertain significance (Mar 20, 2023) | ||
| 5-134115927-G-A | not specified | Uncertain significance (Feb 10, 2022) | ||
| 5-134115951-C-T | not specified | Uncertain significance (Sep 06, 2022) | ||
| 5-134115953-G-A | not specified | Uncertain significance (Dec 20, 2023) | ||
| 5-134115961-C-T | Likely benign (Jan 01, 2023) | |||
| 5-134115994-C-T | Likely benign (Mar 01, 2023) | |||
| 5-134138065-G-A | not specified | Uncertain significance (Jun 02, 2023) | ||
| 5-134138075-C-A | not specified | Uncertain significance (Oct 14, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TCF7 | protein_coding | protein_coding | ENST00000342854 | 10 | 37155 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00537 | 0.990 | 125713 | 0 | 34 | 125747 | 0.000135 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.506 | 173 | 193 | 0.898 | 0.0000109 | 2456 |
| Missense in Polyphen | 68 | 101.23 | 0.67176 | 1074 | ||
| Synonymous | -1.77 | 104 | 83.5 | 1.25 | 0.00000546 | 767 |
| Loss of Function | 2.47 | 7 | 18.5 | 0.379 | 8.83e-7 | 229 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000163 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000575 | 0.0000544 |
| Finnish | 0.000752 | 0.000739 |
| European (Non-Finnish) | 0.000107 | 0.000105 |
| Middle Eastern | 0.0000575 | 0.0000544 |
| South Asian | 0.0000685 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional activator involved in T-cell lymphocyte differentiation. Necessary for the survival of CD4(+) CD8(+) immature thymocytes. Isoforms lacking the N-terminal CTNNB1 binding domain cannot fulfill this role. Binds to the T- lymphocyte-specific enhancer element (5'-WWCAAAG-3') found in the promoter of the CD3E gene. May also act as feedback transcriptional repressor of CTNNB1 and TCF7L2 target genes. TLE1, TLE2, TLE3 and TLE4 repress transactivation mediated by TCF7 and CTNNB1.;
- Pathway
- Gastric cancer - Homo sapiens (human);Adherens junction - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Acute myeloid leukemia - Homo sapiens (human);Breast cancer - Homo sapiens (human);Basal cell carcinoma - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Thyroid cancer - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);Melanogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Arrhythmogenic Right Ventricular Cardiomyopathy;Endoderm Differentiation;Amplification and Expansion of Oncogenic Pathways as Metastatic Traits;miRNA regulation of prostate cancer signaling pathways;Wnt Signaling Pathway and Pluripotency;Endometrial cancer;Chromosomal and microsatellite instability in colorectal cancer;Wnt Signaling Pathway;DNA Damage Response (only ATM dependent);Degradation of beta-catenin by the destruction complex;Signaling by WNT;Signal Transduction;Gene expression (Transcription);RUNX3 regulates WNT signaling;Transcriptional regulation by RUNX3;Generic Transcription Pathway;Repression of WNT target genes;RNA Polymerase II Transcription;Deactivation of the beta-catenin transactivating complex;Ca2+ pathway;Beta-catenin independent WNT signaling;Wnt Canonical;Regulation of nuclear beta catenin signaling and target gene transcription;Binding of TCF/LEF:CTNNB1 to target gene promoters;Formation of the beta-catenin:TCF transactivating complex;TCF dependent signaling in response to WNT;Wnt Mammals
(Consensus)
Intolerance Scores
- loftool
- 0.0491
- rvis_EVS
- 0.11
- rvis_percentile_EVS
- 62
Haploinsufficiency Scores
- pHI
- 0.176
- hipred
- Y
- hipred_score
- 0.726
- ghis
- 0.397
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.860
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tcf7
- Phenotype
- homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; neoplasm; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- tcf7
- Affected structure
- pectoral fin
- Phenotype tag
- abnormal
- Phenotype quality
- undulate
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;immune response;neural tube development;embryonic genitalia morphogenesis;T cell receptor V(D)J recombination;regulation of cell population proliferation;canonical Wnt signaling pathway involved in negative regulation of apoptotic process;alpha-beta T cell differentiation;embryonic digestive tract morphogenesis;embryonic hindgut morphogenesis;canonical Wnt signaling pathway;cellular response to interleukin-4;beta-catenin-TCF complex assembly
- Cellular component
- nucleus;nucleoplasm;transcription factor complex;nuclear euchromatin;nuclear body
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;beta-catenin binding;sequence-specific DNA binding;transcription regulatory region DNA binding