GATA1
GATA binding protein 1, the group of GATA zinc finger domain containing
Basic information
Region (hg38): X:48786540-48794311
Previous symbols: [ "GF1" ]
Links
Phenotypes
GenCC
Source:
- thrombocytopenia, X-linked, with or without dyserythropoietic anemia (Moderate), mode of inheritance: XL
- beta-thalassemia-X-linked thrombocytopenia syndrome (Moderate), mode of inheritance: XL
- Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
- thrombocytopenia with congenital dyserythropoietic anemia (Supportive), mode of inheritance: XL
- cutaneous porphyria (Supportive), mode of inheritance: AR
- beta-thalassemia-X-linked thrombocytopenia syndrome (Supportive), mode of inheritance: XL
- X-linked dyserythropoetic anemia with abnormal platelets and neutropenia (Supportive), mode of inheritance: XL
- thrombocytopenia, X-linked, with or without dyserythropoietic anemia (Strong), mode of inheritance: XL
- GATA1-Related X-Linked Cytopenia (Definitive), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Thrombocytopenia with beta-thalessemia, X-linked; Anemia, X-linked, with or without thrombocytopenia and platelet abnormalities; Dyserythropoietic anemia with thrombocytopenia; Anemia, congenital, nonspherocytic hemolytic, 9 | XL | Hematologic; Pharmacogenomic | Individuals, especially males (though females have been reported with bleeding complications, such as in the postpartum period), may require preventive measures and treatment (eg, with platelet and/or RBC transfusions) related to bleeding diathesis; Certain activities and agents (eg, contact sports and medications such as NSAIDS) should be avoided in some individuals; BMT has been reported; Individuals with Anemia, congenital, nonspherocytic hemolytic, 9 have been reported as requiring RBC transfusions | Hematologic | 871527; 10700180; 11418466; 11675338; 11809723; 12200364; 17209061; 20301538; 22102271; 35030251 |
ClinVar
This is a list of variants' phenotypes submitted to
- GATA_binding_protein_1_related_thrombocytopenia_with_dyserythropoiesis (308 variants)
- Diamond-Blackfan_anemia (307 variants)
- not_provided (60 variants)
- Thrombocytopenia,_X-linked,_with_or_without_dyserythropoietic_anemia (28 variants)
- Inborn_genetic_diseases (26 variants)
- GATA1-related_disorder (25 variants)
- X-linked_dyserythropoetic_anemia_with_abnormal_platelets_and_neutropenia (23 variants)
- Beta-thalassemia-X-linked_thrombocytopenia_syndrome (16 variants)
- not_specified (16 variants)
- Transient_myeloproliferative_syndrome (11 variants)
- Hemolytic_anemia_due_to_erythrocyte_adenosine_deaminase_overproduction (9 variants)
- Down_syndrome (7 variants)
- Acute_megakaryoblastic_leukemia_in_down_syndrome (6 variants)
- Thrombocytopenia (4 variants)
- Macrothrombocytopenia (2 variants)
- Thrombocytopenia,_X-linked,_without_dyserythropoietic_anemia (2 variants)
- Thrombocytopenia,_X-linked,_with_dyserythropoietic_anemia (2 variants)
- Cutaneous_porphyria (1 variants)
- Anemia (1 variants)
- LEUKEMIA,_MEGAKARYOBLASTIC,_OF_DOWN_SYNDROME,_SOMATIC (1 variants)
- Acute_megakaryoblastic_leukemia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GATA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002049.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 72 | 11 | 87 | |||
| missense | 10 | 11 | 156 | 19 | 12 | 208 |
| nonsense | 8 | |||||
| start loss | 4 | 1 | 5 | |||
| frameshift | 33 | 43 | ||||
| splice donor/acceptor (+/-2bp) | 8 | |||||
| Total | 57 | 24 | 164 | 91 | 23 |
Highest pathogenic variant AF is 0.00000895087
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GATA1 | protein_coding | protein_coding | ENST00000376670 | 5 | 7755 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.948 | 0.0519 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.14 | 133 | 175 | 0.759 | 0.0000143 | 2583 |
| Missense in Polyphen | 43 | 72.294 | 0.5948 | 1046 | ||
| Synonymous | 0.108 | 75 | 76.2 | 0.984 | 0.00000634 | 959 |
| Loss of Function | 2.83 | 0 | 9.32 | 0.00 | 6.44e-7 | 164 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional activator or repressor which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence 5'-[AT]GATA[AG]-3' within regulatory regions of globin genes and of other genes expressed in erythroid cells. Activates the transcription of genes involved in erythroid differentiation of K562 erythroleukemia cells, including HBB, HBG1/2, ALAS2 and HMBS (PubMed:24245781). {ECO:0000269|PubMed:22235304, ECO:0000269|PubMed:24245781}.;
- Disease
- DISEASE: X-linked dyserythropoietic anemia and thrombocytopenia (XDAT) [MIM:300367]: Disorder characterized by erythrocytes with abnormal size and shape, and paucity of platelets in peripheral blood. The bone marrow contains abundant and abnormally small megakaryocytes. {ECO:0000269|PubMed:10700180, ECO:0000269|PubMed:11418466, ECO:0000269|PubMed:11675338, ECO:0000269|PubMed:11809723}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thrombocytopenia with beta-thalassemia, X-linked (XLTT) [MIM:314050]: An unusual form of thrombocytopenia associated with beta-thalassemia. Patients have splenomegaly and petechiae, moderate thrombocytopenia, prolonged bleeding time due to platelet dysfunction, reticulocytosis and unbalanced (hemo)globin chain synthesis resembling that of beta-thalassemia minor. {ECO:0000269|PubMed:12200364}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Anemia without thrombocytopenia, X-linked (XLAWT) [MIM:300835]: A form of anemia characterized by abnormal morphology of erythrocytes and granulocytes in peripheral blood, bone marrow dysplasia with hypocellularity of erythroid and granulocytic lineages, and normal or increased number of megakaryocytes. Neutropenia of a variable degree is present in affected individuals. {ECO:0000269|PubMed:16783379}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Hematopoietic Stem Cell Differentiation;Gene expression (Transcription);hemoglobins chaperone;Generic Transcription Pathway;Factors involved in megakaryocyte development and platelet production;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;p73 transcription factor network;Signaling events mediated by HDAC Class II;Hemostasis;C-MYB transcription factor network;RUNX1 regulates transcription of genes involved in differentiation of HSCs;Notch-mediated HES/HEY network;Transcriptional regulation by RUNX1;Signaling events mediated by HDAC Class I
(Consensus)
Recessive Scores
- pRec
- 0.709
Intolerance Scores
- loftool
- 0.0369
- rvis_EVS
- -0.6
- rvis_percentile_EVS
- 17.75
Haploinsufficiency Scores
- pHI
- 0.337
- hipred
- Y
- hipred_score
- 0.697
- ghis
- 0.459
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gata1
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; 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); liver/biliary system phenotype; respiratory system phenotype; immune system phenotype; skeleton 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); normal 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); embryo phenotype;
Zebrafish Information Network
- Gene name
- gata1a
- Affected structure
- myeloid cell
- Phenotype tag
- abnormal
- Phenotype quality
- increased amount
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;in utero embryonic development;transcription by RNA polymerase II;cell-cell signaling;blood coagulation;negative regulation of cell population proliferation;male gonad development;regulation of glycoprotein biosynthetic process;regulation of definitive erythrocyte differentiation;regulation of primitive erythrocyte differentiation;erythrocyte differentiation;megakaryocyte differentiation;platelet formation;basophil differentiation;eosinophil differentiation;negative regulation of bone mineralization;positive regulation of osteoblast proliferation;embryonic hemopoiesis;eosinophil fate commitment;negative regulation of apoptotic process;positive regulation of erythrocyte differentiation;regulation of megakaryocyte differentiation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;erythrocyte development;homeostasis of number of cells within a tissue;positive regulation of peptidyl-tyrosine phosphorylation;platelet aggregation;transcriptional activation by promoter-enhancer looping;dendritic cell differentiation;cellular response to thyroid hormone stimulus;regulation of hematopoietic stem cell differentiation;negative regulation of transcription regulatory region DNA binding;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
- Cellular component
- nucleus;nucleoplasm;transcription factor complex;transcriptional repressor complex;protein-DNA complex
- Molecular function
- transcription regulatory region sequence-specific DNA binding;RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter 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 transcription factor binding;DNA-binding transcription activator activity, RNA polymerase II-specific;p53 binding;DNA binding;DNA-binding transcription factor activity;protein binding;zinc ion binding;chromatin DNA binding;sequence-specific DNA binding;C2H2 zinc finger domain binding