TFDP1
transcription factor Dp-1, the group of Transcription factor Dp family
Basic information
Region (hg38): 13:113584721-113641473
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 TFDP1 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 | |||||
| missense | 16 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 2 | 2 |
Variants in TFDP1
This is a list of pathogenic ClinVar variants found in the TFDP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 13-113611016-C-T | Benign (Dec 31, 2019) | |||
| 13-113611017-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 13-113623227-G-A | not specified | Uncertain significance (Mar 20, 2023) | ||
| 13-113623275-G-A | not specified | Likely benign (Jul 05, 2023) | ||
| 13-113633222-A-C | not specified | Uncertain significance (Mar 05, 2024) | ||
| 13-113633266-A-T | not specified | Uncertain significance (Feb 16, 2023) | ||
| 13-113635993-A-G | not specified | Uncertain significance (Nov 03, 2022) | ||
| 13-113636016-G-A | not specified | Uncertain significance (Dec 20, 2023) | ||
| 13-113636018-G-A | Benign (Dec 31, 2019) | |||
| 13-113636033-C-G | not specified | Uncertain significance (Sep 22, 2023) | ||
| 13-113636055-G-C | not specified | Uncertain significance (Mar 08, 2024) | ||
| 13-113636079-G-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| 13-113636562-A-G | not specified | Uncertain significance (Jan 04, 2024) | ||
| 13-113636616-G-A | not specified | Uncertain significance (Jun 29, 2022) | ||
| 13-113636643-G-A | not specified | Uncertain significance (Sep 01, 2021) | ||
| 13-113637854-C-T | not specified | Uncertain significance (Oct 13, 2021) | ||
| 13-113637877-G-A | not specified | Uncertain significance (Oct 04, 2022) | ||
| 13-113640225-C-G | not specified | Uncertain significance (Jun 01, 2023) | ||
| 13-113640228-G-C | not specified | Likely benign (Jul 15, 2021) | ||
| 13-113640262-G-A | not specified | Uncertain significance (Dec 19, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TFDP1 | protein_coding | protein_coding | ENST00000375370 | 11 | 56773 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.972 | 0.0283 | 125745 | 0 | 3 | 125748 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.28 | 159 | 263 | 0.604 | 0.0000165 | 2710 |
| Missense in Polyphen | 21 | 66.742 | 0.31464 | 806 | ||
| Synonymous | 1.08 | 100 | 115 | 0.872 | 0.00000883 | 781 |
| Loss of Function | 3.71 | 2 | 19.8 | 0.101 | 8.40e-7 | 239 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000615 |
| Ashkenazi Jewish | 0.000106 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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 (PubMed:8405995, PubMed:7739537). 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:0000269|PubMed:20176812, ECO:0000269|PubMed:7739537, ECO:0000269|PubMed:8405995}.;
- Pathway
- TGF-beta signaling pathway - Homo sapiens (human);Cell cycle - Homo sapiens (human);Cell Cycle;Retinoblastoma (RB) in Cancer;regulation of p27 phosphorylation during cell cycle progression;TGF-beta Signaling Pathway;G1 to S cell cycle control;Signal Transduction;Gene expression (Transcription);Inhibition of replication initiation of damaged DNA by RB1/E2F1;cyclin e destruction pathway;influence of ras and rho proteins on g1 to s transition;il-2 receptor beta chain in t cell activation;cell cycle: g1/s check point;cyclins and cell cycle regulation;e2f1 destruction pathway;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;Direct p53 effectors;Cell Cycle;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Cell Cycle, Mitotic;Regulation of retinoblastoma protein;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.272
Intolerance Scores
- loftool
- 0.136
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 7.94
Haploinsufficiency Scores
- pHI
- 0.203
- hipred
- Y
- hipred_score
- 0.681
- ghis
- 0.709
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.976
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tfdp1
- 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); embryo phenotype; growth/size/body region 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);
Gene ontology
- Biological process
- regulation of transcription involved in G1/S transition of mitotic cell cycle;regulation of transcription by RNA polymerase II;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;cell population proliferation;epidermis development;anoikis;positive regulation of transcription by RNA polymerase II;negative regulation of G0 to G1 transition;negative regulation of fat cell proliferation;positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway;regulation of DNA biosynthetic process
- Cellular component
- nucleus;nucleoplasm;mitochondrion;cytosol;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 transcription factor activity;transcription coactivator activity;protein binding;transcription factor binding;protein domain specific binding