TFAP2D

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

Basic information

Region (hg38): 6:50713526-50773033

Previous symbols: [ "TFAP2BL1" ]

Links

ENSG00000008197 ∙ NCBI:83741 ∙ OMIM:610161 ∙ HGNC:15581 ∙ Uniprot:Q7Z6R9 ∙ 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 TFAP2D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFAP2D 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					2	2
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	2

Variants in TFAP2D

This is a list of pathogenic ClinVar variants found in the TFAP2D region.

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

Position	Type	Phenotype	Significance	ClinVar
6-50715177-C-T		not specified	Uncertain significance (Nov 17, 2022)
6-50715321-A-G		not specified	Uncertain significance (Aug 14, 2023)
6-50715519-T-C		not specified	Uncertain significance (Jun 03, 2024)
6-50715560-C-T		not specified	Uncertain significance (Feb 23, 2023)
6-50715604-C-G		not specified	Uncertain significance (Jun 07, 2023)
6-50719148-G-T		not specified	Uncertain significance (Dec 01, 2022)
6-50729227-A-G			Benign/Likely benign (Oct 01, 2024)
6-50745225-A-G			Benign (Apr 17, 2018)
6-50751234-A-G		not specified	Uncertain significance (Sep 12, 2023)
6-50772709-C-A		not specified	Uncertain significance (Jul 05, 2022)
6-50772719-T-G		not specified	Uncertain significance (May 08, 2023)
6-50772767-C-T		not specified	Uncertain significance (Nov 18, 2022)
6-50772786-T-A		not specified	Uncertain significance (Mar 25, 2024)
6-50772791-A-C		not specified	Uncertain significance (Feb 13, 2024)
6-50772802-G-A		not specified	Uncertain significance (Jun 16, 2024)
6-50772802-G-T		not specified	Uncertain significance (Apr 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFAP2D	protein_coding	protein_coding	ENST00000008391	8	59161

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00801	125742	0	3	125745	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.750	214	247	0.866	0.0000127	2906
Missense in Polyphen		49	73.712	0.66475		850
Synonymous	-2.08	127	100	1.26	0.00000539	928
Loss of Function	3.81	1	18.8	0.0531	7.98e-7	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
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 (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: 0.140

Intolerance Scores

• loftool: 0.0231
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.751
• hipred: Y
• hipred_score: 0.783
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.645

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tfap2d
• Phenotype: cellular 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;negative regulation of neuron apoptotic process;positive regulation of transcription by RNA polymerase II;inferior colliculus development
• Cellular component: nucleus;transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific