TFAP2E
Basic information
Region (hg38): 1:35573314-35595328
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 TFAP2E 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 | 40 | 40 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 40 | 0 | 0 |
Variants in TFAP2E
This is a list of pathogenic ClinVar variants found in the TFAP2E region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-35573936-G-C | not specified | Uncertain significance (Apr 09, 2024) | ||
1-35573946-G-A | not specified | Uncertain significance (May 11, 2022) | ||
1-35573985-A-C | not specified | Uncertain significance (Aug 04, 2021) | ||
1-35573996-G-A | not specified | Uncertain significance (Dec 13, 2021) | ||
1-35573996-G-C | not specified | Uncertain significance (Feb 28, 2023) | ||
1-35573997-G-A | not specified | Uncertain significance (Mar 26, 2024) | ||
1-35574041-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
1-35574114-C-A | not specified | Uncertain significance (Apr 18, 2023) | ||
1-35574153-G-A | not specified | Uncertain significance (Nov 28, 2023) | ||
1-35574161-G-C | not specified | Uncertain significance (Feb 28, 2023) | ||
1-35574162-C-T | not specified | Uncertain significance (Mar 25, 2022) | ||
1-35574194-G-A | not specified | Uncertain significance (Oct 27, 2022) | ||
1-35574195-C-T | not specified | Uncertain significance (Oct 27, 2022) | ||
1-35574218-G-T | not specified | Uncertain significance (Aug 16, 2021) | ||
1-35574229-C-A | not specified | Uncertain significance (Nov 28, 2023) | ||
1-35574229-C-G | not specified | Uncertain significance (Dec 21, 2022) | ||
1-35574237-C-T | not specified | Uncertain significance (Nov 28, 2023) | ||
1-35574267-C-T | not specified | Uncertain significance (Mar 24, 2023) | ||
1-35574297-C-T | not specified | Uncertain significance (Jan 17, 2024) | ||
1-35574308-C-T | not specified | Uncertain significance (Aug 08, 2022) | ||
1-35574335-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
1-35574344-G-T | not specified | Uncertain significance (Nov 21, 2023) | ||
1-35574381-C-G | not specified | Uncertain significance (Mar 25, 2024) | ||
1-35574381-C-T | not specified | Uncertain significance (Jul 13, 2021) | ||
1-35574399-A-G | not specified | Uncertain significance (Jun 30, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TFAP2E | protein_coding | protein_coding | ENST00000373235 | 7 | 21959 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000245 | 0.764 | 125720 | 0 | 28 | 125748 | 0.000111 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.02 | 184 | 227 | 0.810 | 0.0000150 | 2725 |
Missense in Polyphen | 96 | 99.386 | 0.96593 | 964 | ||
Synonymous | 0.120 | 103 | 105 | 0.985 | 0.00000740 | 990 |
Loss of Function | 1.15 | 9 | 13.6 | 0.664 | 7.29e-7 | 179 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000559 | 0.000544 |
Ashkenazi Jewish | 0.000129 | 0.0000992 |
East Asian | 0.00 | 0.00 |
Finnish | 0.000191 | 0.000185 |
European (Non-Finnish) | 0.0000638 | 0.0000615 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000156 | 0.000131 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes. AP-2 factors bind to the consensus sequence 5'-GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development. They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC. AP-2-epsilon may play a role in the development of the CNS and in cartilage differentiation (By similarity). {ECO:0000250}.;
- Pathway
- Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Activation of the TFAP2 (AP-2) family of transcription factors;Negative regulation of activity of TFAP2 (AP-2) family transcription factors;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors
(Consensus)
Recessive Scores
- pRec
- 0.116
Haploinsufficiency Scores
- pHI
- 0.158
- hipred
- N
- hipred_score
- 0.301
- ghis
- 0.478
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.833
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tfap2e
- 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);
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein homodimerization activity;protein heterodimerization activity