MT1E

protein-coding

metallothionein 1E, the group of Metallothioneins

Gene summary

Predicted to enable zinc ion binding activity. Involved in cellular response to cadmium ion and cellular response to zinc ion. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

MANE transcript

NM_001363555.2

Inheritance

—

ClinVar variants

U:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr16:56,625,475-56,627,112

External References & Databases

Ensembl (ENSG00000169715)

Transcript & Mutation Effects

hg38 • Region Span ~1.6 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 MT1E variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001363555.2. 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			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	1	0	0	1

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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_001363555.2	RefSeq	NP_001350484.1	2	MANE Select
ENST00000330439.7	Ensembl	ENSP00000328137.6	2	MANE Select
NM_175617.4	RefSeq	NP_783316.2	3	Standard
ENST00000306061.10	Ensembl	ENSP00000307706.5	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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: ENST00000306061
Coding exons: 3
Length: 1638
Individuals with no LoFs: 125743
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125745
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.345	41	35.2	1.16	0.00000191	395
Missense (PolyPhen)		5	5.9635	0.83843		52
Synonymous	-0.0685	15	14.7	1.02	9.63e-7	101
Loss of Function	0.236	2	2.39	0.835	1.03e-7	27

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

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: 0.156

Intolerance Scores

LoFtool: 0.453
RVIS EVS: 0.44
RVIS percentile EVS: 77.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.273

Gene Damage Prediction

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