MTA3

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

Basic information

Region (hg38): 2:42494569-42756947

Links

ENSG00000057935 ∙ NCBI:57504 ∙ OMIM:609050 ∙ HGNC:23784 ∙ Uniprot:Q9BTC8 ∙ 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 MTA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTA3 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						0
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in MTA3

This is a list of pathogenic ClinVar variants found in the MTA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-42568765-G-T		not specified	Uncertain significance (Oct 03, 2022)
2-42579177-T-C		not specified	Uncertain significance (Oct 22, 2021)
2-42609464-T-C		not specified	Uncertain significance (Mar 13, 2023)
2-42609470-A-C		not specified	Uncertain significance (Oct 27, 2023)
2-42640216-T-G		not specified	Uncertain significance (Feb 07, 2023)
2-42644131-C-A		not specified	Uncertain significance (Oct 11, 2024)
2-42644157-C-G		not specified	Uncertain significance (Feb 26, 2024)
2-42644226-C-T		not specified	Uncertain significance (Mar 12, 2024)
2-42644233-T-C		not specified	Uncertain significance (Feb 05, 2024)
2-42656214-A-G		not specified	Uncertain significance (Apr 16, 2024)
2-42656235-G-A		not specified	Uncertain significance (Sep 27, 2021)
2-42656241-G-A		not specified	Uncertain significance (Aug 27, 2024)
2-42656301-C-T		not specified	Uncertain significance (Oct 24, 2024)
2-42659795-G-A		Short stature	Likely pathogenic (Nov 18, 2001)
2-42682488-T-C		not specified	Uncertain significance (May 06, 2024)
2-42682498-A-T		not specified	Uncertain significance (Nov 14, 2024)
2-42704212-C-G		not specified	Uncertain significance (Oct 13, 2023)
2-42704218-A-G		not specified	Uncertain significance (Aug 21, 2023)
2-42704285-C-T		not specified	Uncertain significance (May 26, 2024)
2-42704289-T-G		not specified	Uncertain significance (Apr 11, 2023)
2-42707945-T-C		not specified	Uncertain significance (Apr 08, 2022)
2-42708026-A-G		not specified	Uncertain significance (Aug 26, 2024)
2-42708916-G-C		not specified	Uncertain significance (Dec 28, 2023)
2-42708941-G-A		not specified	Uncertain significance (May 24, 2024)
2-42708964-C-T		not specified	Uncertain significance (Aug 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTA3	protein_coding	protein_coding	ENST00000407270	14	262379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0343	0.966	124629	0	8	124637	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.658	233	263	0.886	0.0000141	3342
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.0000570	0.0000556
Finnish	0.0000476	0.0000464
European (Non-Finnish)	0.0000360	0.0000354
Middle Eastern	0.0000570	0.0000556
South Asian	0.0000339	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Preimplantation Embryo;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);downregulated of mta-3 in er-negative breast tumors;HDACs deacetylate histones;RNA Polymerase I Promoter Clearance;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;Intracellular signaling by second messengers (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.290
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.830
• hipred: Y
• hipred_score: 0.814
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mta3
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: mta3
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• 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;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm;cytoplasm;NuRD complex;intracellular membrane-bounded organelle
• 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;histone deacetylase activity;protein binding;zinc ion binding;histone deacetylase binding;sequence-specific DNA binding;protein-containing complex binding