MT1B

protein-coding

metallothionein 1B, the group of Metallothioneins

Gene summary

The protein encoded by this gene binds heavy metals and protects against toxicity from heavy metal ions. This gene is found in a cluster of similar genes on chromosome 16. [provided by RefSeq, Jul 2016]

Previous symbols:

MT1
MT1Q

MANE transcript

NM_005947.3

Inheritance

—

ClinVar variants

U:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.11

Max pathogenic AF

—

Genomic locus

chr16:56,651,886-56,653,204

External References & Databases

Ensembl (ENSG00000169688)

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 MT1B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005947.3. 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			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	0	0	16

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005947.3	RefSeq	NP_005938.1	3	MANE Select
ENST00000334346.3	Ensembl	ENSP00000334998.2	3	MANE Select
ENST00000562399.1	Ensembl	ENSP00000456056.1	3	Standard
ENST00000562399.2	Ensembl	ENSP00000456056.1	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: ENST00000334346
Coding exons: 3
Length: 1306
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125748
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0152	34	34.3	0.993	0.00000184	388
Missense (PolyPhen)		16	11.542	1.3863		147
Synonymous	0.824	10	13.9	0.719	8.60e-7	103
Loss of Function	-0.161	3	2.71	1.11	1.15e-7	32

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)	0.000018	0.000018	rare
South Asian	0.000065	0.000065	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: 0.170

Intolerance Scores

LoFtool: 0.451
RVIS EVS: 0.41
RVIS percentile EVS: 76.67

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.347

Gene Damage Prediction

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