MTF2

metal response element binding transcription factor 2, the group of Tudor domain containing|PHD finger proteins

Basic information

Region (hg38): 1:93079235-93139079

Links

ENSG00000143033 ∙ NCBI:22823 ∙ OMIM:609882 ∙ HGNC:29535 ∙ Uniprot:Q9Y483 ∙ 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 MTF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTF2 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	15	0	1

Variants in MTF2

This is a list of pathogenic ClinVar variants found in the MTF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-93110243-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-93110247-G-C		not specified	Uncertain significance (Aug 09, 2021)
1-93110261-C-T		not specified	Uncertain significance (Nov 14, 2023)
1-93110373-A-G		not specified	Uncertain significance (Apr 08, 2022)
1-93115020-G-C		not specified	Uncertain significance (Dec 20, 2021)
1-93115023-T-A		not specified	Uncertain significance (May 29, 2024)
1-93115077-A-T		not specified	Uncertain significance (Dec 19, 2022)
1-93118449-G-A			Benign (Feb 12, 2018)
1-93120560-C-T		not specified	Uncertain significance (Apr 23, 2024)
1-93133724-A-C		not specified	Uncertain significance (May 13, 2024)
1-93133783-T-A		not specified	Uncertain significance (Oct 28, 2024)
1-93133940-A-G		not specified	Likely benign (Oct 22, 2024)
1-93133949-A-G		not specified	Uncertain significance (Sep 20, 2023)
1-93133977-T-C		not specified	Uncertain significance (Mar 29, 2022)
1-93134110-C-T		not specified	Uncertain significance (Aug 16, 2022)
1-93134120-A-G		not specified	Uncertain significance (Nov 19, 2024)
1-93134131-G-A		not specified	Uncertain significance (Mar 25, 2024)
1-93134152-A-G		not specified	Uncertain significance (Jun 22, 2024)
1-93136695-C-T		not specified	Uncertain significance (Jun 07, 2024)
1-93136749-C-A		not specified	Uncertain significance (May 14, 2024)
1-93136802-T-G		not specified	Uncertain significance (Apr 03, 2023)
1-93136828-A-G		not specified	Uncertain significance (Jan 08, 2024)
1-93136951-G-A		not specified	Uncertain significance (Jan 25, 2024)
1-93136984-A-G		not specified	Uncertain significance (Feb 23, 2023)
1-93136998-G-A		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTF2	protein_coding	protein_coding	ENST00000370298	15	59847

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000132	125637	0	2	125639	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.55	189	316	0.597	0.0000160	3871
Missense in Polyphen		18	90.259	0.19943		1129
Synonymous	-0.0634	105	104	1.01	0.00000495	1086
Loss of Function	5.11	2	34.3	0.0584	0.00000168	446

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000935	0.00000880
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Polycomb group (PcG) that specifically binds histone H3 trimethylated at 'Lys-36' (H3K36me3) and recruits the PRC2 complex. Acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting the PRC2 complex, leading to enhance PRC2 H3K27me3 methylation activity. Regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. Promotes recruitment of the PRC2 complex to the inactive X chromosome in differentiating XX ES cells and PRC2 recruitment to target genes in undifferentiated ES cells. Required to repress Hox genes by enhancing H3K27me3 methylation of the PRC2 complex. In some conditions may act as an inhibitor of PRC2 activity: able to activate the CDKN2A gene and promote cellular senescence by suppressing the catalytic activity of the PRC2 complex locally. Binds to the metal-regulating-element (MRE) of MT1A gene promoter (By similarity). {ECO:0000250}.
• Pathway: Mesodermal Commitment Pathway;Interactome of polycomb repressive complex 2 (PRC2);Copper homeostasis;Epigenetic regulation of gene expression;Gene expression (Transcription);PRC2 methylates histones and DNA (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.311
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.935
• hipred: Y
• hipred_score: 0.775
• ghis: 0.674

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtf2
• Phenotype: cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; skeleton 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); limbs/digits/tail phenotype; 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); reproductive system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin organization;segment specification;stem cell population maintenance;negative regulation of gene expression, epigenetic;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;stem cell differentiation;negative regulation of histone H3-K27 methylation;positive regulation of histone H3-K27 methylation;cellular response to leukemia inhibitory factor
• Cellular component: nucleus;nucleoplasm;cytoplasm;focal adhesion;ESC/E(Z) complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity;nucleosome binding;methylated histone binding;sequence-specific DNA binding;metal ion binding