GATAD2A

protein-coding

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

Gene summary

Enables protein-macromolecule adaptor activity. Involved in chromatin remodeling and negative regulation of DNA-templated transcription. Located in nucleoplasm. Part of NuRD complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001384528.1

Inheritance

ClinVar variants

P:1U:120B:9

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr19:19,385,826-19,508,932

External References & Databases

Ensembl (ENSG00000167491)

Transcript & Mutation Effects

hg38 • Region Span ~123.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GATAD2A variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 5

GATAD2A-associated neurodevelopmental disorderTotal: 5

GATAD2A-related disorderTotal: 3

Neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001384528.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar		4
missense			113 clinvar	7 clinvar		120
nonsense			1 clinvar			1
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	1	120	9	0	130

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 144 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001384528.1	RefSeq	NP_001371457.1	11	MANE Select
ENST00000683918.1	Ensembl	ENSP00000508398.1	11	MANE Select
NM_001300946.3	RefSeq	NP_001287875.1	11	Standard
NM_001359631.2	RefSeq	NP_001346560.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

negative regulation of transcription by RNA polymerase II
DNA methylation
negative regulation of transcription, DNA-templated

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
protein binding
zinc ion binding
protein binding, bridging
sequence-specific DNA binding

Cellular Component

nucleus
nucleoplasm
NuRD complex
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360315
Coding exons: 11
Length: 123106
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125743
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.27	351	425	0.826	0.0000288	4043
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool: 0.224
RVIS EVS: -0.95
RVIS percentile EVS: 9.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: E
Indispensability score: 0.972

Gene Damage Prediction

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