MT1M

protein-coding

metallothionein 1M, the group of Metallothioneins

Gene summary

This gene encodes a member of the metallothionein superfamily, type 1 family. Metallothioneins have a high content of cysteine residues that bind various heavy metals. These genes are transcriptionally regulated by both heavy metals and glucocorticoids. [provided by RefSeq, Oct 2011]

Previous symbols:

MT1
MT1K

MANE transcript

NM_176870.3

Inheritance

—

ClinVar variants

U:12B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.26

Max pathogenic AF

—

Genomic locus

chr16:56,632,659-56,633,981

External References & Databases

Ensembl (ENSG00000205364)

Transcript & Mutation Effects

hg38 • Region Span ~1.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MT1M variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_176870.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			11 clinvar	2 clinvar		13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	12	2	0	14

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_176870.3	RefSeq	NP_789846.2	3	MANE Select
ENST00000379818.4	Ensembl	ENSP00000369146.3	3	MANE Select
ENST00000570233.1	Ensembl	ENSP00000457575.1	2	Standard
ENST00000858452.1	Ensembl	ENSP00000528511.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Mineral absorption - Homo sapiens (human)
Zinc homeostasis
Response to metal ions
Cellular responses to external stimuli
Metallothioneins bind metals

Biological Process

cellular zinc ion homeostasis
detoxification of copper ion
negative regulation of growth
cellular response to cadmium ion
cellular response to copper ion

Molecular Function

zinc ion binding
metal ion binding

Cellular Component

nucleus
cytoplasm
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379818
Coding exons: 3
Length: 1754
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125722
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.09	52	34.1	1.53	0.00000180	396
Missense (PolyPhen)		12	4.956	2.4213		43
Synonymous	-0.246	16	14.8	1.08	9.64e-7	102
Loss of Function	-0.366	3	2.39	1.26	1.03e-7	27

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.0357

Intolerance Scores

LoFtool: 0.708
RVIS EVS: 0.35
RVIS percentile EVS: 73.97

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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