MT1G

metallothionein 1G, the group of Metallothioneins

Basic information

Region (hg38): 16:56666730-56668065

Previous symbols: [ "MT1" ]

Links

ENSG00000125144 ∙ NCBI:4495 ∙ OMIM:156353 ∙ HGNC:7399 ∙ Uniprot:P13640 ∙ 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 MT1G gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MT1G 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in MT1G

This is a list of pathogenic ClinVar variants found in the MT1G region.

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

Position	Type	Phenotype	Significance	ClinVar
16-56666884-C-T		not specified	Uncertain significance (Jun 17, 2024)
16-56666902-C-T		not specified	Uncertain significance (Sep 16, 2021)
16-56666946-C-G		not specified	Uncertain significance (Dec 01, 2022)
16-56666950-C-T		not specified	Uncertain significance (Sep 29, 2023)
16-56666970-C-G		not specified	Uncertain significance (Feb 16, 2023)
16-56667339-C-T		not specified	Uncertain significance (Sep 25, 2024)
16-56667371-G-A		not specified	Uncertain significance (Apr 24, 2024)
16-56667983-T-C		not specified	Uncertain significance (Mar 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MT1G	protein_coding	protein_coding	ENST00000444837	3	1335

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0322	0.624	125727	0	11	125738	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.800	48	34.7	1.38	0.00000172	401
Missense in Polyphen
Synonymous	-0.185	15	14.1	1.06	8.70e-7	98
Loss of Function	0.262	2	2.44	0.819	1.03e-7	30

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000703	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Metallothioneins have a high content of cysteine residues that bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids.
• Pathway: Mineral absorption - Homo sapiens (human);Copper homeostasis;Zinc homeostasis;Response to metal ions;Cellular responses to external stimuli;Metallothioneins bind metals (Consensus)

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.180
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mt1
• Phenotype: vision/eye phenotype; digestive/alimentary 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); skeleton phenotype; renal/urinary system phenotype; immune system phenotype; liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; 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); hematopoietic system phenotype; growth/size/body region phenotype; reproductive system phenotype; 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); homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: cellular zinc ion homeostasis;detoxification of copper ion;monocyte differentiation;cellular response to vascular endothelial growth factor stimulus;monocyte activation;negative regulation of growth;cellular response to cadmium ion;cellular response to copper ion;cellular response to zinc ion
• Cellular component: nucleus;cytoplasm;perinuclear region of cytoplasm
• Molecular function: protein binding;zinc ion binding;metal ion binding