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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital heart defects, multiple types, 5	AD	Cardiovascular	Individuals have been described with findins including arrhythmias (atrial fibrillation), and awareness may allow prompt diagnosis and management	Cardiovascular	22483626; 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.

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.

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			1	120	5	126
missense			225	7	2	234
nonsense			1			1
start loss			1			1
frameshift			6			6
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			9	8	1	18
non coding			2	60	16	78
Total	0	0	237	187	23

Variants in GATA5

This is a list of pathogenic ClinVar variants found in the GATA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-62464564-G-T			Likely benign (Mar 31, 2019)
20-62464606-T-C			Likely benign (Sep 16, 2018)
20-62464848-C-T			Likely benign (Sep 08, 2023)
20-62464849-A-G			Uncertain significance (Jul 01, 2016)
20-62464851-C-T			Likely benign (May 23, 2024)
20-62464852-G-A		GATA5-related disorder	Uncertain significance (Jul 03, 2023)
20-62464855-C-T		not specified • Congenital heart defects, multiple types, 5	Uncertain significance (Oct 06, 2024)
20-62464857-C-G		not specified	Uncertain significance (Apr 20, 2022)
20-62464858-C-G			Uncertain significance (Dec 02, 2022)
20-62464860-G-A			Likely benign (Apr 26, 2023)
20-62464860-G-C		GATA5-related disorder	Likely benign (Jan 30, 2025)
20-62464861-G-A			Uncertain significance (Oct 18, 2022)
20-62464861-G-T			Uncertain significance (Feb 24, 2024)
20-62464862-C-A		GATA5-related disorder	Uncertain significance (Sep 13, 2022)
20-62464865-C-T			Uncertain significance (Aug 15, 2024)
20-62464870-C-A			Uncertain significance (Jul 28, 2023)
20-62464870-C-T			Uncertain significance (Apr 10, 2024)
20-62464871-G-A		Aortic valve disease 1;Familial thoracic aortic aneurysm and aortic dissection	Uncertain significance (Oct 16, 2024)
20-62464876-GC-G			Uncertain significance (Sep 13, 2024)
20-62464876-G-GC			Uncertain significance (May 20, 2024)
20-62464877-C-A			Uncertain significance (Mar 26, 2023)
20-62464878-C-A			Likely benign (Aug 13, 2024)
20-62464881-C-A		not specified	Likely benign (Nov 18, 2022)
20-62464881-C-G			Uncertain significance (Jul 30, 2024)
20-62464881-CCT-C			Uncertain significance (Apr 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GATA5	protein_coding	protein_coding	ENST00000252997	6	12474

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.285	0.711	125365	0	10	125375	0.0000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	146	187	0.780	0.0000123	2433
Missense in Polyphen		59	86.821	0.67956		955
Synonymous	-0.0269	85	84.7	1.00	0.00000600	844
Loss of Function	2.46	3	12.3	0.243	6.15e-7	154

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000306	0.0000306
Ashkenazi Jewish	0.00	0.00
East Asian	0.000123	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000477	0.0000442
Middle Eastern	0.000123	0.000109
South Asian	0.0000697	0.0000653
Other	0.00	0.00

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

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

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