GATAD2A

GATA zinc finger domain containing 2A, the group of GATA zinc finger domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:19385826-19508932

Links

ENSG00000167491 ∙ NCBI:54815 ∙ OMIM:614997 ∙ HGNC:29989 ∙ Uniprot:Q86YP4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GATAD2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GATAD2A 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		1
missense			69	3		72
nonsense			1			1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	1	70	4	0

Variants in GATAD2A

This is a list of pathogenic ClinVar variants found in the GATAD2A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19465365-G-A		not specified	Uncertain significance (Sep 21, 2023)
19-19465383-G-A		not specified	Uncertain significance (Aug 26, 2024)
19-19465386-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-19465512-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-19465583-G-A		not specified	Uncertain significance (Oct 12, 2021)
19-19465601-C-T		not specified	Uncertain significance (Aug 08, 2022)
19-19465602-G-A		not specified	Uncertain significance (Aug 17, 2021)
19-19465611-A-C		not specified	Uncertain significance (Nov 25, 2024)
19-19492306-T-C		not specified	Likely benign (Jun 23, 2023)
19-19492319-G-A		not specified	Uncertain significance (Aug 16, 2021)
19-19492358-G-A		not specified	Uncertain significance (Dec 03, 2024)
19-19492362-A-G		not specified	Uncertain significance (Jul 17, 2023)
19-19492383-G-A		not specified	Uncertain significance (Feb 08, 2023)
19-19492406-G-T		not specified	Uncertain significance (Jun 04, 2024)
19-19492407-C-T		not specified	Uncertain significance (Jun 04, 2024)
19-19492419-C-T		not specified	Uncertain significance (Oct 03, 2024)
19-19492425-C-T		not specified	Uncertain significance (Mar 14, 2025)
19-19492587-A-T		not specified	Uncertain significance (Oct 17, 2023)
19-19492606-G-T		not specified	Uncertain significance (May 25, 2022)
19-19492656-G-A		not specified	Uncertain significance (Apr 26, 2024)
19-19492680-A-G		not specified	Uncertain significance (May 18, 2022)
19-19492704-G-A		not specified	Likely benign (Mar 15, 2024)
19-19494318-G-A		not specified	Uncertain significance (Nov 09, 2024)
19-19494328-C-G		not specified	Uncertain significance (Jan 10, 2022)
19-19494366-G-A		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GATAD2A	protein_coding	protein_coding	ENST00000360315	11	123106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000430	125735	0	8	125743	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	351	425	0.826	0.0000288	4043
Missense in Polyphen		96	144.01	0.66664		1359
Synonymous	-1.15	212	192	1.11	0.0000146	1365
Loss of Function	4.83	2	31.1	0.0643	0.00000187	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.000111	0.000109
South Asian	0.00	0.00
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. Enhances MBD2-mediated repression. Efficient repression requires the presence of GATAD2B. {ECO:0000269|PubMed:12183469, ECO:0000269|PubMed:16415179}.
• Pathway: ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;Signal Transduction;Epigenetic regulation of gene expression;Gene expression (Transcription);Generic Transcription Pathway;HDACs deacetylate histones;RNA Polymerase I Promoter Clearance;RNA Polymerase II Transcription;Chromatin modifying enzymes;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Chromatin organization;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Intracellular signaling by second messengers;Signaling events mediated by HDAC Class I (Consensus)

Intolerance Scores

• loftool: 0.224
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.27

Haploinsufficiency Scores

• pHI: 0.341
• hipred: Y
• hipred_score: 0.783
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.972

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gatad2a
• 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); 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); 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; growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;DNA methylation;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;NuRD complex;nuclear speck
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;zinc ion binding;protein binding, bridging;sequence-specific DNA binding