MT2A

metallothionein 2A, the group of Metallothioneins

Basic information

Region (hg38): 16:56608584-56609497

Previous symbols: [ "MT2" ]

Links

ENSG00000125148

∙ NCBI:4502 ∙ OMIM:156360 ∙ HGNC:7406 ∙ Uniprot:P02795 ∙ 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 MT2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MT2A 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in MT2A

This is a list of pathogenic ClinVar variants found in the MT2A region.

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

Position	Phenotype	Significance	ClinVar
16-56609016-C-T	not specified	Uncertain significance (Apr 27, 2024)	3296504
16-56609274-T-G	not specified	Uncertain significance (Jul 12, 2023)	2611327
16-56609311-G-A	not specified	Uncertain significance (Apr 07, 2022)	2281984

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MT2A	protein_coding	protein_coding	ENST00000245185	3	1299

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000123	0.122	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.454	27	34.5	0.783	0.00000149	401
Missense in Polyphen		3	5.4888	0.54657		50
Synonymous	0.535	11	13.5	0.815	6.06e-7	98
Loss of Function	-1.31	6	3.40	1.77	1.43e-7	44

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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);Platinum Pathway, Pharmacokinetics/Pharmacodynamics;Copper homeostasis;Zinc homeostasis;Lung fibrosis;Cytokine Signaling in Immune system;Immune System;Response to metal ions;Cellular responses to external stimuli;Interferon gamma signaling;Metallothioneins bind metals;Interferon Signaling;AP-1 transcription factor network (Consensus)

Recessive Scores

pRec: 0.267

Intolerance Scores

loftool: 0.679
rvis_EVS: 0.12
rvis_percentile_EVS: 62.38

Haploinsufficiency Scores

pHI: 0.0870
hipred: N
hipred_score: 0.146
ghis: 0.516

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.960

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mt2
Phenotype: cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; neoplasm; endocrine/exocrine gland 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); digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system 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); normal phenotype; reproductive system phenotype; 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);

Zebrafish Information Network

Gene name: mt2
Affected structure: intersegmental vessel
Phenotype tag: abnormal
Phenotype quality: malformed

Gene ontology

Biological process: cellular copper ion homeostasis;cellular zinc ion homeostasis;response to metal ion;detoxification of copper ion;cellular response to drug;cellular response to interleukin-3;cellular response to erythropoietin;negative regulation of growth;interferon-gamma-mediated signaling pathway;cellular response to cadmium ion;cellular response to copper ion;cellular response to zinc ion
Cellular component: nucleus;cytoplasm;cytosol;perinuclear region of cytoplasm
Molecular function: protein binding;drug binding;zinc ion binding;metal ion binding