MT1B

Summary

MT1B (metallothionein 1B, HGNC:7394) is a protein-coding gene on chromosome 16q13, encoding Metallothionein-1B (P07438). Metallothioneins have a high content of cysteine residues that bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids.

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.

Source: NCBI Gene 4490 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_005947

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7394
Approved symbol	MT1B
Name	metallothionein 1B
Location	16q13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000169688
Ensembl biotype	protein_coding
OMIM	156349
Entrez	4490

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000334346, ENST00000562399

RefSeq mRNA: 1 — MANE Select: NM_005947 NM_005947

CCDS: CCDS10765

Canonical transcript exons

ENST00000334346 — 3 exons

Exon	Start	End
ENSE00001347553	56651886	56651981
ENSE00003475502	56652974	56653204
ENSE00003580835	56652571	56652636

Expression profiles

Bgee: expression breadth broad, 74 present calls, max score 68.18.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2704 / max 324.5459, expressed in 28 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
154249	0.2704	28

Top tissues by expression

121 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	68.18	gold quality
liver	UBERON:0002107	60.01	gold quality
duodenum	UBERON:0002114	55.53	gold quality
vermiform appendix	UBERON:0001154	42.74	gold quality
omental fat pad	UBERON:0010414	37.34	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
esophagus mucosa	UBERON:0002469	30.74	gold quality
left uterine tube	UBERON:0001303	30.63	gold quality
adipose tissue	UBERON:0001013	30.53	gold quality
urinary bladder	UBERON:0001255	30.03	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.32	gold quality
islet of Langerhans	UBERON:0000006	29.16	gold quality
muscle of leg	UBERON:0001383	29.03	gold quality
gastrocnemius	UBERON:0001388	28.73	gold quality
blood	UBERON:0000178	28.23	gold quality
endometrium	UBERON:0001295	28.00	silver quality
prostate gland	UBERON:0002367	27.88	gold quality
lymph node	UBERON:0000029	27.57	gold quality
pancreas	UBERON:0001264	27.51	gold quality
adult mammalian kidney	UBERON:0000082	27.41	gold quality
tonsil	UBERON:0002372	27.05	gold quality
left coronary artery	UBERON:0001626	26.70	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting MT1B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-6830-3P	98.62	68.07	1760
HSA-MIR-654-3P	98.38	67.61	905
HSA-MIR-5585-3P	98.25	67.41	941
HSA-MIR-1279	97.83	67.50	1898
HSA-MIR-1278	97.75	67.55	628
HSA-MIR-3192-5P	96.98	65.76	1926
HSA-MIR-1231	95.10	65.63	663

Literature-anchored findings (GeneRIF, showing 1)

• Eight MT genes were up-regulated after treatment of T-ALL cells with 0.15 and 1.5 microg/mL of metal ores. Copper/cadmium/zinc ore binding. (PMID:15747776)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio	mt2	ENSDARG00000041623

Paralogs (11): MT3 (ENSG00000087250), MT4 (ENSG00000102891), MT1G (ENSG00000125144), MT2A (ENSG00000125148), MT1E (ENSG00000169715), MT1X (ENSG00000187193), MT1F (ENSG00000198417), MT1H (ENSG00000205358), MT1A (ENSG00000205362), MT1M (ENSG00000205364), MT1HL1 (ENSG00000244020)

Protein

Protein identifiers

Metallothionein-1B — P07438 (reviewed: P07438)

Alternative names: Metallothionein-IB

All UniProt accessions (2): P07438, H3BR34

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. Monomer.

Domain organisation. Class I metallothioneins contain 2 metal-binding domains: four divalent ions are chelated within cluster A of the alpha domain and are coordinated via cysteinyl thiolate bridges to 11 cysteine ligands. Cluster B, the corresponding region within the beta domain, can ligate three divalent ions to 9 cysteines.

Similarity. Belongs to the metallothionein superfamily. Type 1 family.

RefSeq proteins (1): NP_005938* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000006	Metalthion_vert	Family
IPR017854	Metalthion_dom_sf	Homologous_superfamily
IPR018064	Metalthion_vert_metal_BS	Binding_site
IPR023587	Metalthion_dom_sf_vert	Homologous_superfamily

Pfam: PF00131

UniProt features (31 total): binding site 28, region of interest 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P07438-F1	77.62	0.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (28): 21; 24; 24; 26; 29; 33; 34; 34; 36; 37; 37; 41 …

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-5661231	Metallothioneins bind metals
R-HSA-5660526	Response to metal ions
R-HSA-8953897	Cellular responses to stimuli

MSigDB gene sets: 75 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOBP_RESPONSE_TO_ZINC_ION, GRUETZMANN_PANCREATIC_CANCER_DN, GOBP_CELLULAR_RESPONSE_TO_CADMIUM_ION, GOBP_GROWTH, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, GOBP_RESPONSE_TO_COPPER_ION, LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, GOBP_RESPONSE_TO_METAL_ION, GOBP_DETOXIFICATION, GOBP_CELLULAR_RESPONSE_TO_ZINC_ION, MORF_BMPR2, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN, GOBP_MONOATOMIC_ION_HOMEOSTASIS

GO Biological Process (6): intracellular zinc ion homeostasis (GO:0006882), detoxification of copper ion (GO:0010273), negative regulation of growth (GO:0045926), cellular response to cadmium ion (GO:0071276), cellular response to copper ion (GO:0071280), cellular response to zinc ion (GO:0071294)

GO Molecular Function (3): zinc ion binding (GO:0008270), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Response to metal ions	1
Cellular responses to stimuli	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular response to metal ion	3
intracellular monoatomic cation homeostasis	1
inorganic ion homeostasis	1
detoxification of inorganic compound	1
stress response to copper ion	1
growth	1
regulation of growth	1
negative regulation of biological process	1
response to cadmium ion	1
response to copper ion	1
response to zinc ion	1
transition metal ion binding	1
cation binding	1
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

196 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MT1B	APRT	P07741	565
MT1B	NQO1	P15559	534
MT1B	GSR	P00390	510
MT1B	PLA2G2A	P14555	494
MT1B	SLC30A1	Q9Y6M5	448
MT1B	PTPN1	P18031	426
MT1B	ATP7B	P35670	394
MT1B	MTF1	Q14872	384
MT1B	A0A494C0M2	A0A494C0M2	370
MT1B	MAP1S	Q66K74	350
MT1B	LRRC63	Q05C16	349
MT1B	LEFTY2	O00292	348
MT1B	GPX4	P36969	326
MT1B	MT1F	P04733	317
MT1B	MT1G	P13640	314

IntAct

16 interactions, top by confidence:

A	B	Type	Score
MT1B	KRTAP10-6	psi-mi:“MI:0915”(physical association)	0.560
MT1B	KRTAP1-1	psi-mi:“MI:0915”(physical association)	0.560
MT1B	KRTAP5-2	psi-mi:“MI:0915”(physical association)	0.560
MT1B	KRTAP17-1	psi-mi:“MI:0915”(physical association)	0.560
MT1B	SMCP	psi-mi:“MI:0915”(physical association)	0.560
MT1B	KRTAP10-6	psi-mi:“MI:0915”(physical association)	0.000
MT1B	KRTAP1-1	psi-mi:“MI:0915”(physical association)	0.000
MT1B	KRTAP5-2	psi-mi:“MI:0915”(physical association)	0.000
MT1B	SMCP	psi-mi:“MI:0915”(physical association)	0.000
MT1B	KRTAP17-1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): MT1B (Two-hybrid), KRTAP17-1 (Two-hybrid), KRTAP10-6 (Two-hybrid), KRTAP1-1 (Two-hybrid), KRTAP5-2 (Two-hybrid), MT1B (Affinity Capture-RNA)

ESM2 similar proteins: A1L3X4, O18842, O42152, P02797, P02798, P02800, P02801, P02802, P02803, P02804, P04355, P04731, P04733, P07438, P09577, P09578, P0DM35, P11957, P13640, P14425, P15786, P17808, P18055, P25713, P27087, P37360, P55942, P55943, P55944, P58280, P67981, P67982, P67983, P68041, P68301, P68302, P68303, P68304, P79376, P79377

Diamond homologs: O18842, O19000, P02795, P02797, P02798, P02800, P02801, P02802, P02803, P02804, P04355, P04731, P04732, P04733, P07438, P09577, P09578, P0DM35, P11957, P13640, P14425, P17808, P18055, P47944, P47945, P49068, P55942, P55943, P58280, P67981, P67982, P67983, P68041, P68301, P68302, P68303, P68304, P79376, P79377, P79378

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

16 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	15
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

281 predictions. Top by Δscore:

Variant	Effect	Δscore
16:56652632:G:GT	donor_gain	1.0000
16:56652632:GAAGT:G	donor_gain	1.0000
16:56652635:GT:G	donor_gain	1.0000
16:56652637:G:GG	donor_gain	1.0000
16:56651983:T:A	donor_loss	0.9900
16:56652702:GCCC:G	donor_gain	0.9900
16:56652558:C:CA	acceptor_gain	0.9800
16:56652569:A:AG	acceptor_gain	0.9800
16:56652570:G:GG	acceptor_gain	0.9800
16:56652659:G:GT	donor_gain	0.9800
16:56652674:GC:G	donor_gain	0.9800
16:56652689:G:T	donor_gain	0.9800
16:56653107:G:GG	donor_gain	0.9800
16:56652565:TTGCA:T	acceptor_loss	0.9700
16:56652566:TGCA:T	acceptor_loss	0.9700
16:56652567:GCAGG:G	acceptor_loss	0.9700
16:56652568:CA:C	acceptor_loss	0.9700
16:56652569:AGGT:A	acceptor_gain	0.9700
16:56652570:GGTG:G	acceptor_gain	0.9700
16:56652684:G:GT	donor_gain	0.9700
16:56652569:AGGTG:A	acceptor_gain	0.9600
16:56652570:GGT:G	acceptor_gain	0.9600
16:56652570:GGTGG:G	acceptor_gain	0.9600
16:56651982:G:GG	donor_gain	0.9500
16:56652566:T:TA	acceptor_gain	0.9500
16:56652569:AG:A	acceptor_gain	0.9500
16:56652570:GG:G	acceptor_gain	0.9500
16:56652675:C:G	donor_gain	0.9400
16:56652705:C:CG	donor_gain	0.9400
16:56652618:T:G	donor_gain	0.9300

AlphaMissense

392 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1001041686 (16:56653309 T>C), RS1001468004 (16:56653506 G>T), RS1003195071 (16:56652288 A>G,T), RS1004868922 (16:56653163 T>C), RS1005658154 (16:56650316 G>A), RS1006431113 (16:56650495 C>T), RS1006690949 (16:56652853 G>A,C,T), RS1007693717 (16:56651743 G>A), RS1007992615 (16:56653578 A>T), RS1010174886 (16:56649904 T>C), RS1010841719 (16:56652321 G>A), RS1011183961 (16:56652126 C>A,T), RS1012927640 (16:56653267 G>A), RS1015981804 (16:56651493 G>A), RS1016466613 (16:56651756 A>T)

Disease associations

OMIM: gene MIM:156349 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001601_1	Gambling	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004699	gambling behaviour

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

62 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	affects expression, increases abundance, increases expression	8
Cadmium	increases abundance, increases expression	7
cadmium sulfate	increases expression	3
Benzo(a)pyrene	decreases expression, increases expression, increases methylation	3
Silver	increases expression	3
Silver Nitrate	increases expression	3
Zinc	affects cotreatment, increases expression, decreases reaction	3
Copper Sulfate	decreases expression, increases expression	3
sodium arsenite	increases expression	2
cupric chloride	increases expression, increases reaction	2
Arsenic Trioxide	increases expression, decreases expression	2
Copper	affects binding, decreases expression, increases expression	2
Disulfiram	increases reaction, affects binding, decreases expression, increases expression	2
Aflatoxin B1	increases methylation, increases expression	2
Particulate Matter	increases expression	2
ML385	increases expression, affects binding, decreases reaction, increases reaction	1
propionaldehyde	increases expression	1
methoxyacetic acid	increases expression, increases reaction	1
thallium sulfate	affects reaction, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
butyraldehyde	increases expression	1
isoconazole	decreases expression, increases cleavage, affects binding, increases reaction, increases expression (+1 more)	1
pyrrolidine dithiocarbamic acid	affects cotreatment, increases expression	1
ochratoxin A	affects cotreatment, increases expression	1
bleomycetin	increases expression	1
bathocuproine sulfonate	affects cotreatment, increases expression	1
cupric oxide	increases expression	1
lei gong teng	decreases expression	1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediamine	affects cotreatment, increases expression	1
epigallocatechin gallate	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.