MT1X

Chr 16

metallothionein 1X

Also known as: MT-1l, MT1

NCBI Gene: 4501 ENSG00000187193 UniProt: P80297 OMIM: 156359

MT1X encodes metallothionein-1X, a cysteine-rich protein that binds heavy metals including copper, zinc, and cadmium, and may participate in anti-apoptotic signaling pathways. The gene shows very low constraint against loss-of-function variants (pLI 0.0009, LOEUF 1.902), and no well-established Mendelian diseases have been definitively linked to MT1X mutations in the pediatric population based on the provided data.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.90

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.90LOEUF

pLI 0.001

Z-score -0.41

OE 1.25 (0.57–1.90)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.24Z-score

OE missense 0.88 (0.66–1.20)

29 obs / 32.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.25 (0.57–1.90)

0≤0.351.4

Missense OE?0.88 (0.66–1.20)

0≤0.61.4

Synonymous OE?1.14

0≤1.21.6

LoF obs/exp: 4 / 3.2Missense obs/exp: 29 / 32.8Syn Z: -0.39

Background carrier burden — how many people carry a rare variant somewhere in MT1X?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 600

94 rare PASS variants

Rare truncating (LoF)

1 in 790

25 rare PASS variants

Rare synonymous (reference)

1 in 1,200

40 rare PASS variants

Rare missense and truncating variants are carried at similar rates in MT1X; this gene does not show strong loss-of-function constraint by this measure. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 1,800	1 in 730
South Asian	~43k	1 in 260	1 in 1,300
Remaining (unassigned)	~30k	1 in 330	1 in 510
European (Finnish)	~27k	≈ 1 in 6,700	none seen
Admixed American	~22k	1 in 930	1 in 800
African / African American	~21k	1 in 1,700	≈ 1 in 4,200
East Asian	~20k	1 in 800	≈ 1 in 9,900
Ashkenazi Jewish	~13k	≈ 1 in 6,500	none seen
Middle Eastern	~2,884	≈ 1 in 580	1 in 580

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 3 coding exons well covered in gnomAD exomes and genomes.? see exons ↓