MT1F

protein-coding

metallothionein 1F, 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_005949.4

Inheritance

—

ClinVar variants

U:11B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr16:56,657,731-56,660,698

External References & Databases

Ensembl (ENSG00000198417)

Transcript & Mutation Effects

hg38 • Region Span ~3.0 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 MT1F variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 7

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005949.4. 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			7 clinvar		1 clinvar	8
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	11	0	1	12

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005949.4	RefSeq	NP_005940.1	3	MANE Select
ENST00000334350.7	Ensembl	ENSP00000334872.6	3	MANE Select
NM_001301272.2	RefSeq	NP_001288201.1	2	Standard
ENST00000568475.1	Ensembl	ENSP00000456462.1	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
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

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: ENST00000334350
Coding exons: 3
Length: 3005
Individuals with no LoFs: 125707
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 125747
p: 0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.186	38	34.9	1.09	0.00000175	396
Missense (PolyPhen)		9	11.47	0.78467		148
Synonymous	0.356	12	13.7	0.878	8.24e-7	95
Loss of Function	0.607	2	3.17	0.632	1.34e-7	37

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.0013	0.0013	notable
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: 0.149

Intolerance Scores

LoFtool: 0.676
RVIS EVS: 0.61
RVIS percentile EVS: 83.07

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.286

Gene Damage Prediction

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