MTF1

metal regulatory transcription factor 1

Basic information

Region (hg38): 1:37809573-37859592

Links

ENSG00000188786 ∙ NCBI:4520 ∙ OMIM:600172 ∙ HGNC:7428 ∙ Uniprot:Q14872 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal dominant 40 (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MTF1 gene.

• Inborn genetic diseases (20 variants)
• not provided (8 variants)
• Autism spectrum disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTF1 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				3	1	4
missense			20	2	2	24
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	5	3

Variants in MTF1

This is a list of pathogenic ClinVar variants found in the MTF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-37815176-C-A		not specified	Uncertain significance (Jul 12, 2023)
1-37815194-A-G		not specified	Uncertain significance (Jan 06, 2023)
1-37815235-T-C			Likely benign (May 24, 2018)
1-37815302-C-T		not specified	Uncertain significance (Apr 12, 2022)
1-37815335-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-37815345-C-T		not specified	Uncertain significance (Jun 03, 2022)
1-37815365-A-G		not specified	Uncertain significance (Dec 15, 2023)
1-37815374-G-T		not specified	Uncertain significance (Dec 08, 2023)
1-37815426-G-C		not specified	Uncertain significance (May 04, 2022)
1-37822245-G-C		not specified	Uncertain significance (Feb 27, 2024)
1-37822315-T-C		not specified	Uncertain significance (May 23, 2023)
1-37822320-T-G		not specified	Uncertain significance (Oct 14, 2021)
1-37822363-C-T		not specified	Uncertain significance (Mar 31, 2023)
1-37822413-G-A		not specified	Uncertain significance (Dec 06, 2022)
1-37822417-C-T		not specified	Uncertain significance (Aug 12, 2022)
1-37822428-G-A		not specified	Uncertain significance (Feb 26, 2024)
1-37822555-G-A			Likely benign (Dec 31, 2019)
1-37822561-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-37822570-G-A			Benign (Aug 01, 2018)
1-37822600-G-T		not specified	Uncertain significance (Aug 15, 2023)
1-37822637-T-G		not specified	Uncertain significance (May 05, 2022)
1-37822642-A-G		not specified	Uncertain significance (Nov 13, 2023)
1-37822664-C-T			Likely benign (Dec 31, 2019)
1-37823790-G-A			Likely benign (Oct 29, 2018)
1-37832250-T-C		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTF1	protein_coding	protein_coding	ENST00000373036	10	50054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0310	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.54	272	418	0.650	0.0000219	4903
Missense in Polyphen		61	149	0.40939		1748
Synonymous	0.481	159	167	0.953	0.00000951	1547
Loss of Function	4.50	5	32.8	0.152	0.00000190	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activates the metallothionein I promoter. Binds to the metal responsive element (MRE). {ECO:0000269|PubMed:8065932}.
• Pathway: Copper homeostasis;Zinc homeostasis;MTF1 activates gene expression;Response to metal ions;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.0966

Intolerance Scores

• loftool: 0.211
• rvis_EVS: 0.0000761
• rvis_percentile_EVS: 53.98

Haploinsufficiency Scores

• pHI: 0.886
• hipred: Y
• hipred_score: 0.728
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.578

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtf1
• Phenotype: vision/eye 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); immune system phenotype; liver/biliary system phenotype; embryo phenotype; neoplasm; normal 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); hematopoietic system phenotype; 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); growth/size/body region phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;response to oxidative stress;central nervous system development;response to metal ion;positive regulation of transcription by RNA polymerase II;response to cadmium ion
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;histone acetyltransferase binding;metal ion binding