TFAP2C
transcription factor AP-2 gamma, the group of Transcription factor AP-2 family
Basic information
Region (hg38): 20:56629306-56639283
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 TFAP2C 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 | |||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 0 | 1 |
Variants in TFAP2C
This is a list of pathogenic ClinVar variants found in the TFAP2C region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-56631277-A-G | not specified | Uncertain significance (Mar 04, 2024) | ||
| 20-56631279-C-T | Benign (Dec 31, 2019) | |||
| 20-56631289-C-G | not specified | Uncertain significance (May 30, 2024) | ||
| 20-56631317-A-T | not specified | Uncertain significance (May 14, 2024) | ||
| 20-56631433-C-A | not specified | Uncertain significance (Aug 12, 2021) | ||
| 20-56631491-C-T | not specified | Uncertain significance (Mar 11, 2022) | ||
| 20-56631503-C-G | not specified | Uncertain significance (Oct 10, 2023) | ||
| 20-56631562-G-C | not specified | Uncertain significance (Sep 26, 2022) | ||
| 20-56631562-G-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 20-56631641-C-T | not specified | Uncertain significance (Apr 19, 2023) | ||
| 20-56631655-C-T | Microcephaly | Uncertain significance (-) | ||
| 20-56631674-A-G | not specified | Uncertain significance (Oct 14, 2023) | ||
| 20-56631809-T-C | Microcephaly | Uncertain significance (-) | ||
| 20-56633418-A-G | not specified | Uncertain significance (Mar 20, 2024) | ||
| 20-56634215-C-T | not specified | Uncertain significance (Jan 10, 2022) | ||
| 20-56637793-T-A | not specified | Uncertain significance (Sep 28, 2022) | ||
| 20-56637825-T-C | not specified | Uncertain significance (Aug 21, 2023) | ||
| 20-56637825-T-G | not specified | Uncertain significance (Dec 14, 2022) | ||
| 20-56637949-C-G | not specified | Uncertain significance (Jun 17, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TFAP2C | protein_coding | protein_coding | ENST00000201031 | 7 | 9982 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.922 | 0.0779 | 125546 | 0 | 2 | 125548 | 0.00000797 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.46 | 135 | 243 | 0.555 | 0.0000125 | 2872 |
| Missense in Polyphen | 28 | 80.077 | 0.34966 | 946 | ||
| Synonymous | 0.420 | 104 | 110 | 0.949 | 0.00000621 | 917 |
| Loss of Function | 3.37 | 2 | 17.0 | 0.118 | 8.16e-7 | 212 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000616 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000964 | 0.00000881 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| 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. Involved in the MTA1-mediated epigenetic regulation of ESR1 expression in breast cancer. {ECO:0000269|PubMed:11694877, ECO:0000269|PubMed:24413532}.;
- Pathway
- Ectoderm Differentiation;Gene expression (Transcription);Generic Transcription Pathway;SUMOylation of transcription factors;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;RNA Polymerase II Transcription;SUMOylation;Validated transcriptional targets of TAp63 isoforms;Activation of the TFAP2 (AP-2) family of transcription factors;TFAP2 (AP-2) family regulates transcription of growth factors and their receptors;TFAP2 (AP-2) family regulates transcription of other transcription factors;TFAP2 (AP-2) family regulates transcription of cell cycle 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
- 0.283
Intolerance Scores
- loftool
- 0.0352
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 37.11
Haploinsufficiency Scores
- pHI
- 0.907
- hipred
- Y
- hipred_score
- 0.853
- ghis
- 0.557
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tfap2c
- Phenotype
- growth/size/body region phenotype; embryo 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); normal phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;cell-cell signaling;male gonad development;regulation of gene expression, epigenetic;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;nucleoplasm;mitochondrion;cytosol
- 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 repressor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;protein dimerization activity