MT1X

protein-coding

metallothionein 1X, the group of Metallothioneins

Gene summary

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

Previous symbols:

MANE transcript

NM_005952.4

Inheritance

—

ClinVar variants

U:16

Top phenotype

MT1X-related disorder

gnomAD constraint

pLI —, LoF o/e 1.25

Max pathogenic AF

—

Genomic locus

chr16:56,682,470-56,684,196

External References & Databases

Ensembl (ENSG00000187193)

Transcript & Mutation Effects

hg38 • Region Span ~1.7 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 MT1X variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 11

MT1X-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005952.4. 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			1 clinvar			1
missense			11 clinvar			11
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	16	0	0	16

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005952.4	RefSeq	NP_005943.1	3	MANE Select
ENST00000394485.5	Ensembl	ENSP00000377995.4	3	MANE Select
ENST00000562939.1	Ensembl	ENSP00000475791.1	2	Standard
ENST00000562939.2	Ensembl	ENSP00000475791.1	2	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
Oxidative Stress
Response to metal ions

Biological Process

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

Molecular Function

protein binding
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: ENST00000394485
Coding exons: 3
Length: 1773
Individuals with no LoFs: 125615
Homozygous LoFs: 0
Heterozygous LoFs: 124
Defined: 125739
p: 0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.238	29	32.8	0.883	0.00000154	397
Missense (PolyPhen)		4	4.6175	0.86627		44
Synonymous	-0.388	15	13.2	1.14	7.04e-7	101
Loss of Function	-0.413	4	3.20	1.25	1.35e-7	44

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0.0018	0.0018	notable
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00067	0.00067	rare
South Asian	0.00033	0.00033	rare
Other	0.00065	0.00065	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. May be involved in FAM168A anti-apoptotic signaling (PubMed:23251525). {ECO:0000269|PubMed:23251525}.;

Intolerance Scores

LoFtool: 0.721
RVIS EVS: 0.24
RVIS percentile EVS: 68.72

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.575

Gene Damage Prediction

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