TFAP2E

transcription factor AP-2 epsilon, the group of Transcription factor AP-2 family

Basic information

Region (hg38): 1:35573313-35595328

Links

ENSG00000116819 ∙ NCBI:339488 ∙ OMIM:614428 ∙ HGNC:30774 ∙ Uniprot:Q6VUC0 ∙ 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 TFAP2E gene.

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: gnomAD

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: dbNSFP

• 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