ATF2
activating transcription factor 2, the group of Basic leucine zipper proteins|MicroRNA protein coding host genes
Basic information
Region (hg38): 2:175072249-175168382
Previous symbols: [ "CREB2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (15 variants)
- not provided (4 variants)
- not specified (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATF2 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 | 3 | |||||
| missense | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 17 | 1 | 2 |
Variants in ATF2
This is a list of pathogenic ClinVar variants found in the ATF2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-175074624-C-T | Likely benign (Jun 20, 2018) | |||
| 2-175074631-T-C | not specified | Uncertain significance (Oct 05, 2023) | ||
| 2-175074721-G-A | not specified | Uncertain significance (Mar 14, 2023) | ||
| 2-175074723-C-G | not specified | Uncertain significance (Jan 17, 2023) | ||
| 2-175074730-G-A | not specified | Uncertain significance (Oct 29, 2021) | ||
| 2-175074752-T-C | not specified | Uncertain significance (Sep 13, 2023) | ||
| 2-175074803-A-T | not specified | Uncertain significance (Sep 16, 2021) | ||
| 2-175074807-G-A | Benign (Feb 25, 2018) | |||
| 2-175074815-A-T | not specified | Uncertain significance (Dec 22, 2023) | ||
| 2-175080669-C-T | not specified | Uncertain significance (Jul 12, 2022) | ||
| 2-175093160-A-C | Uncertain significance (Jul 28, 2017) | |||
| 2-175093202-G-A | Benign (Feb 25, 2018) | |||
| 2-175093233-C-T | not specified | Uncertain significance (Mar 25, 2015) | ||
| 2-175097458-T-C | not specified | Uncertain significance (Aug 15, 2023) | ||
| 2-175097487-G-A | not specified | Uncertain significance (Jan 31, 2023) | ||
| 2-175114076-T-C | not specified | Uncertain significance (Mar 06, 2023) | ||
| 2-175114798-T-C | not specified | Uncertain significance (Jun 18, 2021) | ||
| 2-175114840-G-T | not specified | Uncertain significance (Mar 29, 2023) | ||
| 2-175118016-G-C | not specified | Uncertain significance (Feb 28, 2023) | ||
| 2-175121490-C-A | not specified | Uncertain significance (Jul 13, 2022) | ||
| 2-175136433-T-C | not specified | Uncertain significance (Apr 04, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATF2 | protein_coding | protein_coding | ENST00000264110 | 12 | 96133 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.991 | 0.00869 | 125735 | 0 | 8 | 125743 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.35 | 164 | 274 | 0.600 | 0.0000137 | 3262 |
| Missense in Polyphen | 24 | 68.812 | 0.34877 | 889 | ||
| Synonymous | 0.176 | 96 | 98.2 | 0.977 | 0.00000503 | 1024 |
| Loss of Function | 4.32 | 3 | 27.4 | 0.109 | 0.00000147 | 314 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000443 | 0.0000440 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional activator which regulates the transcription of various genes, including those involved in anti- apoptosis, cell growth, and DNA damage response. Dependent on its binding partner, binds to CRE (cAMP response element) consensus sequences (5'-TGACGTCA-3') or to AP-1 (activator protein 1) consensus sequences (5'-TGACTCA-3'). In the nucleus, contributes to global transcription and the DNA damage response, in addition to specific transcriptional activities that are related to cell development, proliferation and death. In the cytoplasm, interacts with and perturbs HK1- and VDAC1-containing complexes at the mitochondrial outer membrane, thereby impairing mitochondrial membrane potential, inducing mitochondrial leakage and promoting cell death. The phosphorylated form (mediated by ATM) plays a role in the DNA damage response and is involved in the ionizing radiation (IR)-induced S phase checkpoint control and in the recruitment of the MRN complex into the IR-induced foci (IRIF). Exhibits histone acetyltransferase (HAT) activity which specifically acetylates histones H2B and H4 in vitro. In concert with CUL3 and RBX1, promotes the degradation of KAT5 thereby attenuating its ability to acetylate and activate ATM. Can elicit oncogenic or tumor suppressor activities depending on the tissue or cell type. {ECO:0000269|PubMed:10821277, ECO:0000269|PubMed:15916964, ECO:0000269|PubMed:18397884, ECO:0000269|PubMed:22304920}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Cortisol synthesis and secretion - Homo sapiens (human);Relaxin signaling pathway - Homo sapiens (human);Aldosterone synthesis and secretion - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Thyroid hormone synthesis - Homo sapiens (human);Influenza A - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Amphetamine addiction - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Hepatitis B - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Alcoholism - Homo sapiens (human);Cocaine addiction - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Tacrolimus/Cyclosporine Pathway, Pharmacodynamics;Intracellular Signalling Through Adenosine Receptor A2b and Adenosine;Intracellular Signalling Through Adenosine Receptor A2a and Adenosine;EGF-Core;Energy Metabolism;IL-1 signaling pathway;Angiogenesis overview;B Cell Receptor Signaling Pathway;AGE-RAGE pathway;ATM Signaling Pathway;Structural Pathway of Interleukin 1 (IL-1);Myometrial Relaxation and Contraction Pathways;Photodynamic therapy-induced AP-1 survival signaling.;TGF-beta Signaling Pathway;MAPK Signaling Pathway;ATM Signaling Network in Development and Disease;IL-4 Signaling Pathway;DNA IR-Double Strand Breaks (DSBs) and cellular response via ATM;VEGFA-VEGFR2 Signaling Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Ethanol effects on histone modifications;p38 MAPK Signaling Pathway;PI3K-Akt Signaling Pathway;T-Cell antigen Receptor (TCR) Signaling Pathway;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signal Transduction;Gene expression (Transcription);Signaling by Interleukins;p38 mapk signaling pathway;angiotensin ii mediated activation of jnk pathway via pyk2 dependent signaling;the information processing pathway at the ifn beta enhancer;alk in cardiac myocytes;the 41bb-dependent immune response;mapkinase signaling pathway;Generic Transcription Pathway;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;RNA Polymerase II Transcription;Chromatin modifying enzymes;TCR;Innate Immune System;Immune System;KitReceptor;BMP2 signaling TAK1;ATF-2 transcription factor network;BCR;IL-1 p38;AndrogenReceptor;HATs acetylate histones;IL1;TLR p38;TGF_beta_Receptor;Activation of the AP-1 family of transcription factors;MAPK targets/ Nuclear events mediated by MAP kinases;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;TP53 Regulates Transcription of DNA Repair Genes;ErbB1 downstream signaling;Regulation of PTEN gene transcription;MyD88 dependent cascade initiated on endosome;PTEN Regulation;PIP3 activates AKT signaling;IL2;Signaling by Nuclear Receptors;Chromatin organization;Transcriptional Regulation by TP53;IL4;IL5;TGF-beta signaling TAK1;Estrogen-dependent gene expression;TLR ECSIT MEKK1 p38;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;ESR-mediated signaling;Intracellular signaling by second messengers;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Signaling mediated by p38-alpha and p38-beta;RAC1 signaling pathway;CDC42 signaling events;AP-1 transcription factor network;Regulation of retinoblastoma protein;Regulation of nuclear SMAD2/3 signaling;IL12-mediated signaling events;RhoA signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.281
Intolerance Scores
- loftool
- 0.350
- rvis_EVS
- -0.71
- rvis_percentile_EVS
- 14.4
Haploinsufficiency Scores
- pHI
- 0.882
- hipred
- Y
- hipred_score
- 0.816
- ghis
- 0.720
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atf2
- Phenotype
- vision/eye 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); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; skeleton phenotype; immune system phenotype; respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; neoplasm; 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); normal phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;outflow tract morphogenesis;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;response to osmotic stress;cellular response to DNA damage stimulus;response to water deprivation;positive regulation of gene expression;negative regulation of angiogenesis;histone acetylation;intra-S DNA damage checkpoint;positive regulation of transforming growth factor beta2 production;positive regulation of neuron apoptotic process;fat cell differentiation;positive regulation of transcription by RNA polymerase II;negative regulation of epithelial cell proliferation;regulation of DNA-binding transcription factor activity;positive regulation of DNA-binding transcription factor activity;adipose tissue development;amelogenesis;positive regulation of cardiac muscle myoblast proliferation;positive regulation of mitochondrial membrane permeability involved in apoptotic process
- Cellular component
- nucleus;nucleoplasm;cytoplasm;mitochondrial outer membrane;site of double-strand break
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II activating transcription factor binding;enhancer sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;histone acetyltransferase activity;protein binding;cAMP response element binding protein binding;protein kinase binding;cAMP response element binding;metal ion binding;protein heterodimerization activity