TFDP2

transcription factor Dp-2, the group of Transcription factor Dp family

Basic information

Region (hg38): 3:141944428-142149544

Links

ENSG00000114126

∙ NCBI:7029 ∙ OMIM:602160 ∙ HGNC:11751 ∙ Uniprot:Q14188 ∙ 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 TFDP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFDP2 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			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1 clinvar			1
Total	0	0	17	0	0

Variants in TFDP2

This is a list of pathogenic ClinVar variants found in the TFDP2 region.

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

Position	Phenotype	Significance	ClinVar
3-141952562-T-C	not specified	Uncertain significance (Sep 12, 2023)	2602930
3-141952577-G-T	not specified	Uncertain significance (Jan 23, 2024)	3176499
3-141952675-C-A	not specified	Uncertain significance (Apr 13, 2022)	2283966
3-141952695-C-T	not specified	Uncertain significance (Jul 07, 2022)	2218606
3-141952936-T-C	not specified	Uncertain significance (Feb 14, 2024)	3176498
3-141959685-C-A	not specified	Uncertain significance (Mar 19, 2024)	3325624
3-141959775-C-T	not specified	Uncertain significance (Jun 06, 2023)	2558163
3-141959776-G-A	not specified	Uncertain significance (Apr 07, 2023)	2508321
3-141963899-G-T	not specified	Uncertain significance (Apr 26, 2023)	2541235
3-141963957-C-T	not specified	Uncertain significance (Dec 15, 2023)	3176504
3-141970128-C-T	not specified	Uncertain significance (Oct 16, 2023)	3176503
3-141974065-C-G	not specified	Uncertain significance (Apr 01, 2024)	3325625
3-141978543-T-C	not specified	Uncertain significance (Nov 18, 2023)	3176502
3-141978663-C-T	not specified	Uncertain significance (Nov 19, 2022)	2213006
3-141978677-C-T	not specified	Uncertain significance (Dec 12, 2023)	3176501
3-142005454-A-G	not specified	Uncertain significance (Jun 29, 2022)	3176500
3-142005491-T-C	not specified	Uncertain significance (May 23, 2023)	2518951
3-142005508-G-A	not specified	Uncertain significance (Jul 25, 2023)	2613712
3-142005541-T-C	not specified	Uncertain significance (Mar 24, 2023)	2529407

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFDP2	protein_coding	protein_coding	ENST00000489671	12	205110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000502	121764	0	2	121766	0.00000821

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	156	228	0.685	0.0000113	2893
Missense in Polyphen		44	79.533	0.55323		1038
Synonymous	1.38	72	88.5	0.814	0.00000469	857
Loss of Function	4.57	1	26.3	0.0381	0.00000154	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000583	0.0000567
Finnish	0.00	0.00
European (Non-Finnish)	0.00000975	0.00000894
Middle Eastern	0.0000583	0.0000567
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Can stimulate E2F-dependent transcription. Binds DNA cooperatively with E2F family members through the E2 recognition site, 5'-TTTC[CG]CGC-3', found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The TFDP2:E2F complex functions in the control of cell-cycle progression from G1 to S phase. The E2F1:DP complex appears to mediate both cell proliferation and apoptosis. Blocks adipocyte differentiation by repressing CEBPA binding to its target gene promoters (PubMed:20176812). {ECO:0000305|PubMed:20176812}.;
Pathway: Cell cycle - Homo sapiens (human);Retinoblastoma (RB) in Cancer;G1 to S cell cycle control;Signal Transduction;Gene expression (Transcription);Inhibition of replication initiation of damaged DNA by RB1/E2F1;Transcriptional Regulation by E2F6;Generic Transcription Pathway;Oncogene Induced Senescence;Oxidative Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;RNA Polymerase II Transcription;Activation of NOXA and translocation to mitochondria;Activation of PUMA and translocation to mitochondria;Activation of BH3-only proteins;Intrinsic Pathway for Apoptosis;Transcription of E2F targets under negative control by DREAM complex;Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1;G0 and Early G1;Apoptosis;Programmed Cell Death;Cyclin D associated events in G1;G1 Phase;SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription;Activation of E2F1 target genes at G1/S;G1/S-Specific Transcription;Pre-NOTCH Transcription and Translation;Pre-NOTCH Expression and Processing;E2F mediated regulation of DNA replication;Mitotic G1-G1/S phases;Signaling by NOTCH;Cellular responses to external stimuli;TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest;TGF_beta_Receptor;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;TP53 Regulates Transcription of Cell Cycle Genes;G1/S Transition;Transcriptional Regulation by TP53;Cell Cycle;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Cell Cycle, Mitotic;E2F transcription factor network (Consensus)

Recessive Scores

pRec: 0.182

Intolerance Scores

loftool: 0.483
rvis_EVS: -0.14
rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

pHI: 0.963
hipred: N
hipred_score: 0.481
ghis: 0.581

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tfdp2
Phenotype

Gene ontology

Biological process: regulation of transcription involved in G1/S transition of mitotic cell cycle;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;heart development;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;negative regulation of G0 to G1 transition;positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway
Cellular component: nucleus;nucleoplasm;mitochondrion;RNA polymerase II transcription factor complex
Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;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 coregulator activity;protein binding;transcription factor binding;protein domain specific binding