GeneBe

GATA5

GATA binding protein 5, the group of GATA zinc finger domain containing

Basic information

Region (hg38): 20:62463497-62475995

Links

ENSG00000130700 ∙ NCBI:140628 ∙ OMIM:611496 ∙ HGNC:15802 ∙ Uniprot:Q9BWX5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • tetralogy of fallot (Supportive), mode of inheritance: AD
  • familial atrial fibrillation (Supportive), mode of inheritance: AD
  • familial bicuspid aortic valve (Supportive), mode of inheritance: AD
  • congenital heart defects, multiple types, 5 (Limited), mode of inheritance: Unknown
  • congenital heart defects, multiple types, 5 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Congenital heart defects, multiple types, 5ADCardiovascularIndividuals have been described with findins including arrhythmias (atrial fibrillation), and awareness may allow prompt diagnosis and managementCardiovascular22483626; 22961344; 23031282; 23175127; 23295592; 25543888; 27066509; 28180938
Bi-allelic variants have also been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GATA5 gene.

  • not_provided (502 variants)
  • not_specified (60 variants)
  • Congenital_heart_defects,_multiple_types,_5 (22 variants)
  • GATA5-related_disorder (22 variants)
  • Familial_thoracic_aortic_aneurysm_and_aortic_dissection (4 variants)
  • Congenital_heart_defects,_multiple_types (3 variants)
  • Inborn_genetic_diseases (2 variants)
  • Aortic_valve_disease_1 (1 variants)
  • Arterial_dissection (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GATA5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000080473.5. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
137
clinvar
1
clinvar
 140
missense
4
clinvar
1
clinvar
268
clinvar
17
clinvar
1
clinvar
 291
nonsense
2
clinvar
 2
start loss
1
 1
frameshift
8
clinvar
 8
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 4 1 282 154 2

Highest pathogenic variant AF is 0.0000374572

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GATA5protein_codingprotein_codingENST00000252997 612474
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.2850.7111253650101253750.0000399
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.071461870.7800.00001232433
Missense in Polyphen5986.8210.67956955
Synonymous-0.02698584.71.000.00000600844
Loss of Function2.46312.30.2436.15e-7154

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00003060.0000306
Ashkenazi Jewish0.000.00
East Asian0.0001230.000109
Finnish0.000.00
European (Non-Finnish)0.00004770.0000442
Middle Eastern0.0001230.000109
South Asian0.00006970.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Transcription factor required during cardiovascular development (PubMed:23289003). Plays an important role in the transcriptional program(s) that underlies smooth muscle cell diversity (By similarity). Binds to the functionally important CEF-1 nuclear protein binding site in the cardiac-specific slow/cardiac troponin C transcriptional enhancer (PubMed:25543888). {ECO:0000250|UniProtKB:P97489, ECO:0000269|PubMed:23289003, ECO:0000269|PubMed:25543888}.;
Disease
DISEASE: Congenital heart defects, multiple types, 5 (CHTD5) [MIM:617912]: A disorder characterized by congenital developmental abnormalities involving structures of the heart. Common defects include transposition of the great arteries, aortic stenosis, atrial septal defect, ventricular septal defect, pulmonic stenosis, patent ductus arteriosus, and tetralogy of Fallot. Some patients also have cardiac arrhythmias, which may be due to the anatomic defect itself or to surgical interventions. CHTD5 inheritance can be autosomal dominant or recessive. {ECO:0000269|PubMed:22483626, ECO:0000269|PubMed:22641149, ECO:0000269|PubMed:22961344, ECO:0000269|PubMed:23031282, ECO:0000269|PubMed:23175127, ECO:0000269|PubMed:23289003, ECO:0000269|PubMed:23295592, ECO:0000269|PubMed:24573614, ECO:0000269|PubMed:24638895, ECO:0000269|PubMed:25543888}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Factors involved in megakaryocyte development and platelet production;Hemostasis (Consensus)

Recessive Scores

pRec
0.303

Haploinsufficiency Scores

pHI
0.532
hipred
Y
hipred_score
0.548
ghis
0.433

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.625

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Gata5
Phenotype
skeleton phenotype; renal/urinary system phenotype; immune system phenotype; digestive/alimentary 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); reproductive system 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); homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; endocrine/exocrine gland 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);

Zebrafish Information Network

Gene name
gata5
Affected structure
anatomical system
Phenotype tag
abnormal
Phenotype quality
quality

Gene ontology

Biological process
aortic valve morphogenesis;endocardial cushion fusion;blood coagulation;negative regulation of cardiac muscle hypertrophy;positive regulation of gene expression;negative regulation of gene expression;positive regulation of Notch signaling pathway involved in heart induction;positive regulation of transcription by RNA polymerase II;cardiac muscle tissue development;intestinal epithelial cell differentiation;positive regulation of cardiac endothelial to mesenchymal transition;cellular response to BMP stimulus;circulatory system development;positive regulation of transcription from RNA polymerase II promoter involved in heart development
Cellular component
nuclear chromatin;nucleus;nucleoplasm
Molecular function
RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;zinc ion binding;transcription regulatory region DNA binding