GATAD1

GATA zinc finger domain containing 1, the group of GATA zinc finger domain containing|EMSY complex

Basic information

Region (hg38): 7:92447481-92460075

Links

ENSG00000157259 ∙ NCBI:57798 ∙ OMIM:614518 ∙ HGNC:29941 ∙ Uniprot:Q8WUU5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• dilated cardiomyopathy 2B (Limited), mode of inheritance: AR
• familial isolated dilated cardiomyopathy (Supportive), mode of inheritance: AD
• dilated cardiomyopathy 2B (Limited), mode of inheritance: AR
• dilated cardiomyopathy (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cardiomyopathy, dilated, 2B	AR	Cardiovascular	Surveillance (eg, echocardiography/electocardiography), preventive measures and medical management (including ICD placement) may be helpful to decrease morbidity and mortality	Cardiovascular	21965549

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GATAD1 gene.

• Dilated cardiomyopathy 2B (123 variants)
• Cardiovascular phenotype (96 variants)
• not specified (28 variants)
• not provided (24 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GATAD1 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	49		51
missense			90	1	2	93
nonsense			1			1
start loss						0
frameshift			3			3
inframe indel			3			3
splice donor/acceptor (+/-2bp)			1			1
splice region			3	5		8
non coding			1	25	6	32
Total	0	0	101	75	8

Variants in GATAD1

This is a list of pathogenic ClinVar variants found in the GATAD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-92447513-C-G			Likely benign (Jul 15, 2018)
7-92447690-C-T		not specified	Likely benign (Jun 21, 2017)
7-92447721-C-T			Likely benign (May 16, 2018)
7-92447727-A-G		not specified • Cardiovascular phenotype	Conflicting classifications of pathogenicity (Jul 14, 2021)
7-92447736-C-T		Dilated cardiomyopathy 2B	Likely benign (Jan 04, 2024)
7-92447738-G-A		Cardiovascular phenotype • Dilated cardiomyopathy 2B	Likely benign (Jul 06, 2023)
7-92447748-C-T		Cardiovascular phenotype	Uncertain significance (Jan 02, 2024)
7-92447751-A-T		Dilated cardiomyopathy 2B	Uncertain significance (Aug 02, 2020)
7-92447753-C-T		Cardiovascular phenotype	Likely benign (Jan 31, 2024)
7-92447756-C-T		Dilated cardiomyopathy 2B	Likely benign (Dec 20, 2018)
7-92447760-G-A		Cardiovascular phenotype	Uncertain significance (Jan 13, 2021)
7-92447765-C-T		Dilated cardiomyopathy 2B	Uncertain significance (Jan 03, 2022)
7-92447767-A-G		Dilated cardiomyopathy 2B	Uncertain significance (Sep 12, 2022)
7-92447777-G-A		not specified • Dilated cardiomyopathy 2B • Cardiovascular phenotype	Benign/Likely benign (Jan 08, 2024)
7-92447786-G-A		Dilated cardiomyopathy 2B	Uncertain significance (Dec 06, 2020)
7-92447791-A-G		Dilated cardiomyopathy 2B • Cardiovascular phenotype	Uncertain significance (Nov 11, 2023)
7-92447800-C-T			Uncertain significance (Jan 03, 2017)
7-92447805-G-C		Cardiovascular phenotype	Uncertain significance (May 24, 2022)
7-92447808-G-A		Cardiovascular phenotype	Uncertain significance (Feb 28, 2023)
7-92447813-C-T		Dilated cardiomyopathy 2B	Likely benign (Dec 16, 2022)
7-92447814-C-A		Cardiovascular phenotype	Uncertain significance (Jun 14, 2022)
7-92447816-C-T		Dilated cardiomyopathy 2B • Cardiovascular phenotype	Likely benign (Dec 29, 2022)
7-92447823-C-T		Cardiovascular phenotype	Uncertain significance (Jul 21, 2023)
7-92447825-T-G		not specified • Dilated cardiomyopathy 2B • Cardiovascular phenotype • GATAD1-related disorder	Conflicting classifications of pathogenicity (Dec 04, 2023)
7-92447831-T-C		Dilated cardiomyopathy 2B	Likely benign (Aug 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GATAD1	protein_coding	protein_coding	ENST00000287957	5	11384

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.430	0.564	125738	0	8	125746	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	68	110	0.620	0.00000517	1716
Missense in Polyphen		18	35.759	0.50337		489
Synonymous	-0.735	45	39.1	1.15	0.00000194	545
Loss of Function	2.28	2	9.64	0.207	4.03e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000527	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of some chromatin complex recruited to chromatin sites methylated 'Lys-4' of histone H3 (H3K4me). {ECO:0000269|PubMed:20850016}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.116
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.657
• hipred: N
• hipred_score: 0.380
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gatad1

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;chromatin assembly
• Cellular component: nucleus;nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;zinc ion binding;sequence-specific DNA binding