MTA3

protein-coding

metastasis associated 1 family member 3, the group of GATA zinc finger domain containing|NuRD complex subunits|Myb/SANT domain containing

Gene summary

Predicted to enable histone deacetylase binding activity; transcription coactivator activity; and transcription corepressor 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_001330442.2

Inheritance

—

ClinVar variants

P:1U:60

Top phenotype

Short stature

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr2:42,494,569-42,756,947

External References & Databases

Ensembl (ENSG00000057935)

Transcript & Mutation Effects

hg38 • Region Span ~262.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MTA3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

Short statureTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001330442.2. 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
missense		1 clinvar	57 clinvar			58
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	60	0	0	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 60 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001330442.2	RefSeq	NP_001317371.1	17	MANE Select
ENST00000405094.2	Ensembl	ENSP00000385823.1	17	MANE Select
NM_001282755.2	RefSeq	NP_001269684.1	15	Standard
NM_001282756.2	RefSeq	NP_001269685.1	15	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
mta3	Danio rerio	Structure: nucleate erythrocyte Quality: absent abnormal

Gene / Model

Organism

Observed Phenotype

mta3

Danio rerio

Structure: nucleate erythrocyte

Quality: absent

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Preimplantation Embryo
ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
Positive epigenetic regulation of rRNA expression
Signal Transduction
Epigenetic regulation of gene expression

Biological Process

negative regulation of transcription by RNA polymerase II
positive regulation of cell population proliferation
positive regulation of G2/M transition of mitotic cell cycle
histone deacetylation
negative regulation of transcription, DNA-templated

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
RNA polymerase II repressing transcription factor binding
chromatin binding
transcription coactivator activity
transcription corepressor activity

Cellular Component

nucleus
nucleoplasm
cytoplasm
NuRD complex
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000407270
Coding exons: 14
Length: 262379
Individuals with no LoFs: 124629
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 124637
p: 0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.658	233	263	0.886	0.0000141	3342
Missense (PolyPhen)		43	81.174	0.52973		1042
Synonymous	-1.78	114	92.2	1.24	0.00000489	935
Loss of Function	3.49	8	27.9	0.287	0.00000133	394

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000057	0.000056	rare
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000034	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. Contributes to transcriptional repression by BCL6. {ECO:0000269|PubMed:12705869, ECO:0000269|PubMed:15454082}.;

Recessive Scores

pRec: 0.142

Intolerance Scores

LoFtool: 0.290
RVIS EVS: -0.6
RVIS percentile EVS: 17.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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