MT4

metallothionein 4, the group of Metallothioneins

Basic information

Region (hg38): 16:56565072-56568957

Links

ENSG00000102891 ∙ NCBI:84560 ∙ OMIM:606206 ∙ HGNC:18705 ∙ Uniprot:P47944 ∙ 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 MT4 gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MT4 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in MT4

This is a list of pathogenic ClinVar variants found in the MT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-56565156-T-A		not specified	Uncertain significance (Mar 24, 2023)
16-56567790-C-G		not specified	Uncertain significance (Jan 05, 2022)
16-56568862-C-T		not specified	Uncertain significance (Dec 28, 2022)
16-56568895-G-A		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MT4	protein_coding	protein_coding	ENST00000219162	3	3909

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000131	0.240	125123	0	152	125275	0.000607

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.360	40	34.1	1.17	0.00000169	405
Missense in Polyphen		7	5.7659	1.214		59
Synonymous	-0.383	12	10.4	1.15	5.30e-7	92
Loss of Function	-0.746	5	3.49	1.43	1.46e-7	49

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00124
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000471	0.0000462
European (Non-Finnish)	0.000168	0.000159
Middle Eastern	0.00	0.00
South Asian	0.00376	0.00363
Other	0.000171	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to bind zinc and copper. Could play a special role in regulating zinc metabolism during the differentiation of stratified epithelia.
• Pathway: Copper homeostasis;Zinc homeostasis;Response to metal ions;Cellular responses to external stimuli;Metallothioneins bind metals (Consensus)

Recessive Scores

• pRec: 0.253

Intolerance Scores

• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.27

Haploinsufficiency Scores

• pHI: 0.271
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0211

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mt4

Gene ontology

• Biological process: cellular zinc ion homeostasis;biological_process;detoxification of copper ion;cellular response to cadmium ion;cellular response to copper ion;cellular response to zinc ion
• Cellular component: nucleus;cytoplasm
• Molecular function: metal ion binding