TFAP4

transcription factor AP-4, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 16:4257186-4273075

Links

ENSG00000090447 ∙ NCBI:7023 ∙ OMIM:600743 ∙ HGNC:11745 ∙ Uniprot:Q01664 ∙ 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 TFAP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFAP4 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			11		1	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	11	0	1

Variants in TFAP4

This is a list of pathogenic ClinVar variants found in the TFAP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4258082-C-A		not specified	Uncertain significance (Mar 06, 2023)
16-4258097-G-C		not specified	Uncertain significance (Aug 02, 2023)
16-4258101-A-G		not specified	Uncertain significance (Aug 30, 2022)
16-4258140-T-A		not specified	Uncertain significance (Mar 29, 2022)
16-4258152-G-T		not specified	Uncertain significance (May 30, 2024)
16-4260178-G-A		not specified	Uncertain significance (Aug 13, 2021)
16-4260462-C-T			Benign (Oct 17, 2017)
16-4260482-C-A		not specified	Uncertain significance (Apr 15, 2024)
16-4260516-T-G		not specified	Uncertain significance (Jul 14, 2022)
16-4261915-G-A		not specified	Uncertain significance (Jun 24, 2022)
16-4262346-G-A		not specified	Uncertain significance (Jun 29, 2023)
16-4262561-T-C		not specified	Uncertain significance (May 26, 2024)
16-4262601-T-C		not specified	Uncertain significance (May 17, 2023)
16-4272701-G-C		not specified	Uncertain significance (Dec 28, 2023)
16-4272707-A-T		not specified	Uncertain significance (Mar 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFAP4	protein_coding	protein_coding	ENST00000204517	7	15890

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00269	104262	0	2	104264	0.00000959

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	152	218	0.696	0.0000153	2180
Missense in Polyphen		14	52.905	0.26463		457
Synonymous	-0.277	97	93.6	1.04	0.00000680	676
Loss of Function	3.86	0	17.4	0.00	9.06e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000388	0.0000388
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000415	0.0000415
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that activates both viral and cellular genes by binding to the symmetrical DNA sequence 5'- CAGCTG-3'.
• Pathway: Proteoglycans in cancer - Homo sapiens (human) (Consensus)

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.347
• hipred: Y
• hipred_score: 0.728
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.797

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tfap4
• 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); hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator;negative regulation of cell population proliferation;positive regulation of apoptotic process;negative regulation of DNA binding;negative regulation by host of viral transcription;positive regulation by host of viral transcription;negative regulation of cyclin-dependent protein serine/threonine kinase activity;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;protein-containing complex assembly;negative regulation of cell cycle arrest;cellular response to dexamethasone stimulus;regulation of mitotic cell cycle phase transition;positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway
• Cellular component: nucleus;mitochondrion;transcriptional repressor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;protein homodimerization activity;histone deacetylase binding;sequence-specific DNA binding;transcription regulatory region DNA binding;protein heterodimerization activity;E-box binding