SLC30A1

Summary

SLC30A1 (solute carrier family 30 member 1, HGNC:11012) is a protein-coding gene on chromosome 1q32.3, encoding Proton-coupled zinc antiporter SLC30A1 (Q9Y6M5). Zinc ion:proton antiporter that could function at the plasma membrane mediating zinc efflux from cells against its electrochemical gradient protecting them from intracellular zinc accumulation and toxicity.

Predicted to enable calcium channel inhibitor activity and zinc:proton antiporter activity. Involved in defense response to bacterium; intracellular zinc ion homeostasis; and zinc ion import into organelle. Located in several cellular components, including Golgi apparatus; basolateral plasma membrane; and nuclear membrane.

Source: NCBI Gene 7779 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 29 total
• MANE Select transcript: NM_021194

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11012
Approved symbol	SLC30A1
Name	solute carrier family 30 member 1
Location	1q32.3
Locus type	gene with protein product
Status	Approved
Aliases	ZRC1
Ensembl gene	ENSG00000170385
Ensembl biotype	protein_coding
OMIM	609521
Entrez	7779

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000367001

RefSeq mRNA: 1 — MANE Select: NM_021194 NM_021194

CCDS: CCDS1499

Canonical transcript exons

ENST00000367001 — 2 exons

Exon	Start	End
ENSE00001197164	211577991	211579161
ENSE00001443209	211571568	211576289

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 99.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.4832 / max 162.6780, expressed in 1783 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
17351	6.7487	1713
17348	4.2628	1380
17350	1.7274	950
17349	0.4124	215
17347	0.2639	115
17346	0.0271	6
17345	0.0232	6
17344	0.0176	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
jejunal mucosa	UBERON:0000399	99.02	gold quality
choroid plexus epithelium	UBERON:0003911	98.17	gold quality
caput epididymis	UBERON:0004358	98.17	gold quality
upper leg skin	UBERON:0004262	97.49	gold quality
trabecular bone tissue	UBERON:0002483	96.75	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	96.66	gold quality
mammalian vulva	UBERON:0000997	96.61	gold quality
cartilage tissue	UBERON:0002418	96.59	gold quality
corpus epididymis	UBERON:0004359	96.56	gold quality
penis	UBERON:0000989	96.46	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.39	gold quality
endothelial cell	CL:0000115	96.28	gold quality
parietal pleura	UBERON:0002400	96.21	gold quality
colonic mucosa	UBERON:0000317	95.96	gold quality
germinal epithelium of ovary	UBERON:0001304	95.81	gold quality
skin of hip	UBERON:0001554	95.61	gold quality
pleura	UBERON:0000977	95.33	gold quality
pigmented layer of retina	UBERON:0001782	95.30	gold quality
nephron tubule	UBERON:0001231	95.27	gold quality
duodenum	UBERON:0002114	94.58	gold quality
cauda epididymis	UBERON:0004360	94.54	gold quality
bronchial epithelial cell	CL:0002328	94.34	gold quality
decidua	UBERON:0002450	94.28	gold quality
metanephric glomerulus	UBERON:0004736	94.18	gold quality
adult organism	UBERON:0007023	94.17	gold quality
visceral pleura	UBERON:0002401	94.03	gold quality
pericardium	UBERON:0002407	93.94	gold quality
liver	UBERON:0002107	93.91	gold quality
renal glomerulus	UBERON:0000074	93.89	gold quality
seminal vesicle	UBERON:0000998	92.94	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-9841	yes	1340.84
E-ANND-3	no	2.85

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MTF1

miRNA regulators (miRDB)

51 targeting SLC30A1, 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-4668-3P	100.00	68.74	2635
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-4255	99.72	67.70	1541
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-379-3P	99.69	69.60	1524
HSA-MIR-411-3P	99.69	69.63	1524
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-802	99.61	67.70	1254
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-105-5P	99.54	69.24	2060
HSA-MIR-7853-5P	99.54	69.30	2055

Literature-anchored findings (GeneRIF, showing 32)

• AIDL cells exhibited a lower expression of zinc transporter 1 (ZnT1) and higher expression of ZnT3 than LNCaP cells. (PMID:14662799)
• Our findings therefore indicate that ZnT-1 modulates the permeation of cations through LTCC, thereby, regulating cation homeostasis through this pathway. (PMID:15451416)
• correlation analysis of ZnT-1 levels and senile plaque and neurofibrillary tangle counts of Alzheimer’s disease showed a significant positive correlation (PMID:16179263)
• regulation of ZnT-1 protein in human breast cancer xenografts (PMID:17786585)
• This study provides evidence for increased ZnT-1 expression in atria of patients with atrial fibrillation. (PMID:17971132)
• hZnT-1 is the most regulated zinc exporter in leukocytes. it i sfound in the plasma membrane. (PMID:17971500)
• HPV16 E5 protein binds to EVER and ZnT-1 and blocks their negative regulation (PMID:18158319)
• Data show that ZNT1 is extensively present in the Abeta-positive plaques in the cortex of human AD brains. (PMID:18639746)
• our results suggest that alterations in Zn transport proteins ZnT-1, ZnT-4 and ZnT-6 may contribute to the pathology observed in preclinical Alzheimer’s disease subjects before onset of clinical symptoms (PMID:19371353)
• zinc transporter 1 is an endogenous inhibitor of L-type calcium channels (PMID:19767393)
• The effects of zinc and cadmium on the expression and membrane localization of metallothioneins and ZNT1 in hepatoma cells are reproted. (PMID:19900532)
• ZnT-1 expression was found to be augmented in the atria of atrial tachycardia patients. (PMID:20201890)
• GSPE and EGCG inhibit the expression of zinc-binding metallothioneins and plasma membrane zinc exporter ZnT1 (SLC30A1). (PMID:20471814)
• The metallothionein gene had a higher expression in the blood, when compared to zinc transporters ZnT-1, Zip-1, and Zip-3 (p=0.01 in obese patients. (PMID:21053094)
• Differentiated Caco-2 cells tolerate significantly higher levels of zinc compared to undifferentiated Caco-2 cells, which was accompanied by upregulated ZnT-1 and downregulated ZIP1 levels. (PMID:21103883)
• the transporter ZnT1 at the basolateral membrane, regulate the amount of zinc released to the portal circulation for systemic distribution (PMID:21462106)
• The results of this study showed that signi fi cant positive correlations between ZIP1,ZnT1, and ZnT6 in most brain in patient with Alzheimer’s disease. (PMID:22349685)
• ZnT-1 augments CaV3.1 and CaV3.2 channel signals by stimulating the Ras-ERK pathways. (PMID:22572848)
• Data indicate that the expression levels of ZnT and ZIP families in the three cell lines, when treated with high concentration of ZnSO4, increased and decreased corresponding to their functions, respectively. (PMID:23839533)
• Data indicate that zinc transporters ZnT1 and Zip1 were the most abundantly expressed zinc transporters in leukocytes. (PMID:24488210)
• ZnT-1 extrudes zinc from mammalian cells by functioning as a Zn(2+)/H(+) exchanger. (PMID:24951051)
• MTF1 heads a hierarchy of zinc sensors, and through controlling the expression of a raft of metallothioneins and other key proteins involved in controlling intracellular zinc levels (e.g. ZnT1) alters zinc buffering capacity and total cellular zinc content. (PMID:26824222)
• This study showed that there was a significant increase in protein levels of ZnT1 in the prefrontal cortex in Major depressive disorder, relative to control subjects (PMID:27661418)
• MiRNA-8073 targets ZnT1 to inhibit malignant progression of ovarian cancer. (PMID:31364107)
• SRB1 in macrophages regulates phagocytosis and promotes M1 switch into M2 macrophages, contributing to muscle regeneration. (PMID:31471319)
• Frontline Science: LPS-inducible SLC30A1 drives human macrophage-mediated zinc toxicity against intracellular Escherichia coli. (PMID:32441444)
• The Roles of ZnT1 and ZnT4 in Glucose-Stimulated Zinc Secretion in Prostate Epithelial Cells. (PMID:33140261)
• Increased expression of zinc transporter ZIP4, ZIP11, ZnT1, and ZnT6 predicts poor prognosis in pancreatic cancer. (PMID:33631610)
• Somatic SLC30A1 mutations altering zinc transporter ZnT1 cause aldosterone-producing adenomas and primary aldosteronism. (PMID:37709865)
• Zinc transporter 1 expression in hepatocellular carcinoma correlates with prognosis: A single-center retrospective study. (PMID:38103516)
• Structural insights into the calcium-coupled zinc export of human ZnT1. (PMID:38669333)
• Zinc transporter 1 functions in copper uptake and cuproptosis. (PMID:39111308)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc30a1a	ENSDARG00000005463
danio_rerio	slc30a1b	ENSDARG00000053896
mus_musculus	Slc30a1	ENSMUSG00000037434
rattus_norvegicus	Slc30a1	ENSRNOG00000004749

Paralogs (8): SLC30A4 (ENSG00000104154), SLC30A3 (ENSG00000115194), SLC30A5 (ENSG00000145740), SLC30A6 (ENSG00000152683), SLC30A2 (ENSG00000158014), SLC30A7 (ENSG00000162695), SLC30A8 (ENSG00000164756), SLC30A10 (ENSG00000196660)

Protein

Protein identifiers

Proton-coupled zinc antiporter SLC30A1 — Q9Y6M5 (reviewed: Q9Y6M5)

Alternative names: Solute carrier family 30 member 1, Zinc transporter 1

All UniProt accessions (1): Q9Y6M5

UniProt curated annotations — full annotation on UniProt →

Function. Zinc ion:proton antiporter that could function at the plasma membrane mediating zinc efflux from cells against its electrochemical gradient protecting them from intracellular zinc accumulation and toxicity. Alternatively, could prevent the transport to the plasma membrane of CACNB2, the L-type calcium channels regulatory subunit, through a yet to be defined mechanism. By modulating the expression of these channels at the plasma membrane, could prevent calcium and zinc influx into cells. By the same mechanism, could also prevent L-type calcium channels-mediated heavy metal influx into cells. In some cells, could also function as a zinc ion:proton antiporter mediating zinc entry into the lumen of cytoplasmic vesicles. In macrophages, can increase zinc ions concentration into the lumen of cytoplasmic vesicles containing engulfed bacteria and could help inactivate them. Forms a complex with TMC6/EVER1 and TMC8/EVER2 at the ER membrane of keratynocytes which facilitates zinc uptake into the ER. Down-regulates the activity of transcription factors induced by zinc and cytokines.

Subunit / interactions. Homodimer. Interacts with TMEM163. Interacts and forms a complex with TMC6 and TMC8; the interaction regulates zinc transport into the ER. (Microbial infection) Interacts with human papillomavirus 16/HPV16 protein E5; the interaction alleviates SLC30A1-mediated transcription factors inhibition.

Subcellular location. Cell membrane. Basolateral cell membrane. Cytoplasmic vesicle membrane. Cytoplasm. Endoplasmic reticulum membrane. Golgi apparatus membrane. Nucleus membrane.

Post-translational modifications. N-glycosylated at Asn-299. N-glycosylation promotes endocytosis and degradation through the proteasomal or lysosomal pathways.

Induction. Up-regulated by zinc (at protein level). Up-regulated in macrophages by LPS (at protein level).

Similarity. Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family. SLC30A subfamily.

RefSeq proteins (1): NP_067017* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002524	Cation_efflux	Family
IPR027469	Cation_efflux_TMD_sf	Homologous_superfamily
IPR027470	Cation_efflux_CTD	Domain
IPR036837	Cation_efflux_CTD_sf	Homologous_superfamily
IPR058533	Cation_efflux_TM	Domain

Pfam: PF01545, PF16916

Catalyzed reactions (Rhea), 1 shown:

• Zn(2+)(in) + 2 H(+)(out) = Zn(2+)(out) + 2 H(+)(in) (RHEA:72627)

UniProt features (46 total): helix 13, topological domain 7, transmembrane region 6, strand 6, binding site 4, region of interest 2, compositionally biased region 2, chain 1, modified residue 1, glycosylation site 1, mutagenesis site 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

12 structures.

PDB	Method	Resolution (Å)
9HRS	X-RAY DIFFRACTION	1.92
9IF2	X-RAY DIFFRACTION	2.11
8XMA	ELECTRON MICROSCOPY	2.65
9KZW	ELECTRON MICROSCOPY	3
8ZSB	ELECTRON MICROSCOPY	3.26
8J2G	ELECTRON MICROSCOPY	3.4
8XM6	ELECTRON MICROSCOPY	3.48
8ZSZ	ELECTRON MICROSCOPY	3.59
8XMF	ELECTRON MICROSCOPY	3.64
8ZB0	ELECTRON MICROSCOPY	3.7
9L00	ELECTRON MICROSCOPY	3.78
8XMJ	ELECTRON MICROSCOPY	4.18

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y6M5-F1	67.92	0.32

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 (4): 43; 47; 251; 255

Post-translational modifications (1): 506

Glycosylation sites (1): 299

Mutagenesis-validated functional residues (1):

Position	Phenotype
299	loss of n-glycosylation. no effect on localization to the plasma membrane. increased stability at the plasma membrane. n

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-435368	Zinc efflux and compartmentalization by the SLC30 family

MSigDB gene sets: 366 (showing top): MORF_RAGE, GOBP_DENDRITE_DEVELOPMENT, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_DN, FUNG_IL2_SIGNALING_2, GOBP_NEGATIVE_REGULATION_OF_TRANSMEMBRANE_TRANSPORT, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_RESPONSE_TO_ZINC_ION, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_TRANSITION_METAL_ION_TRANSPORT, GOBP_REGULATION_OF_DENDRITE_MORPHOGENESIS, GOBP_DENDRITIC_SPINE_DEVELOPMENT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, HALMOS_CEBPA_TARGETS_UP, GOBP_NEUROTRANSMITTER_TRANSPORT, GOBP_NEUROGENESIS

GO Biological Process (20): in utero embryonic development (GO:0001701), zinc ion transport (GO:0006829), intracellular calcium ion homeostasis (GO:0006874), intracellular zinc ion homeostasis (GO:0006882), detoxification of zinc ion (GO:0010312), defense response to bacterium (GO:0042742), negative regulation of neurotransmitter secretion (GO:0046929), positive regulation of dendritic spine morphogenesis (GO:0061003), zinc ion import into organelle (GO:0062111), calcium ion import (GO:0070509), cadmium ion transmembrane transport (GO:0070574), zinc ion transmembrane transport (GO:0071577), negative regulation of zinc ion transmembrane import (GO:0071584), detoxification of cadmium ion (GO:0071585), negative regulation of calcium ion import (GO:0090281), zinc export across plasma membrane (GO:0140882), regulation of postsynaptic density protein 95 clustering (GO:1902897), monoatomic ion transport (GO:0006811), monoatomic cation transport (GO:0006812), transmembrane transport (GO:0055085)

GO Molecular Function (7): zinc ion transmembrane transporter activity (GO:0005385), calcium channel inhibitor activity (GO:0019855), metal ion binding (GO:0046872), zinc:proton antiporter activity (GO:0140826), protein binding (GO:0005515), monoatomic cation transmembrane transporter activity (GO:0008324), antiporter activity (GO:0015297)

GO Cellular Component (18): Golgi membrane (GO:0000139), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), membrane (GO:0016020), basolateral plasma membrane (GO:0016323), T-tubule (GO:0030315), dendrite (GO:0030425), cytoplasmic vesicle membrane (GO:0030659), nuclear membrane (GO:0031965), Schaffer collateral - CA1 synapse (GO:0098685), postsynaptic density membrane (GO:0098839), postsynaptic density, intracellular component (GO:0099092), glutamatergic postsynaptic density (GO:0099573), nucleus (GO:0005634), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Zinc transporters	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
zinc ion transmembrane transport	3
monoatomic cation transmembrane transport	3
cellular anatomical structure	3
cytoplasm	3
intracellular membrane-bounded organelle	3
postsynaptic density	3
intracellular monoatomic cation homeostasis	2
detoxification of inorganic compound	2
transport	2
endomembrane system	2
organelle membrane	2
chordate embryonic development	1
transition metal ion transport	1
calcium ion homeostasis	1
inorganic ion homeostasis	1
stress response to zinc ion	1
defense response	1
response to bacterium	1
neurotransmitter secretion	1
regulation of neurotransmitter secretion	1
negative regulation of neurotransmitter transport	1
negative regulation of secretion by cell	1
positive regulation of neuron projection development	1
positive regulation of dendrite morphogenesis	1
dendritic spine morphogenesis	1
positive regulation of dendritic spine development	1
regulation of dendritic spine morphogenesis	1
calcium ion transport	1
cadmium ion transport	1
zinc ion transport	1
zinc ion import across plasma membrane	1
regulation of zinc ion transmembrane import	1
negative regulation of zinc ion transmembrane transport	1
stress response to cadmium ion	1
negative regulation of calcium ion transport	1
calcium ion import	1
regulation of calcium ion import	1
export across plasma membrane	1
postsynaptic density protein 95 clustering	1
regulation of protein localization to membrane	1

Protein interactions and networks

STRING

1337 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC30A1	TMC6	Q7Z403	969
SLC30A1	TMC8	Q8IU68	964
SLC30A1	SLC30A6	Q6NXT4	956
SLC30A1	SLC39A1	Q9NY26	893
SLC30A1	SLC30A9	Q6PML9	810
SLC30A1	SLC39A10	Q9ULF5	804
SLC30A1	SLC39A6	Q13433	797
SLC30A1	H3BSS0	H3BSS0	791
SLC30A1	SLC39A7	Q92504	782
SLC30A1	SLC39A5	Q6ZMH5	756
SLC30A1	SLC39A14	Q15043	755
SLC30A1	SLC39A9	Q9NUM3	748
SLC30A1	SLC39A8	Q9C0K1	748
SLC30A1	SLC39A11	Q8N1S5	732
SLC30A1	SLC39A13	Q96H72	725

IntAct

114 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
STX12	SNAP23	psi-mi:“MI:0914”(association)	0.640
ADGRG5	KLRG2	psi-mi:“MI:0914”(association)	0.530
IL20RA	UPK3BL1	psi-mi:“MI:0914”(association)	0.530
CD83	BTAF1	psi-mi:“MI:0914”(association)	0.530
GALNT6	NDUFS4	psi-mi:“MI:0914”(association)	0.530
STS	GJA1	psi-mi:“MI:0914”(association)	0.530
DIRAS3	MTIF2	psi-mi:“MI:0914”(association)	0.530
SLC31A1	C2orf72	psi-mi:“MI:0914”(association)	0.530
CSGALNACT2	GOLIM4	psi-mi:“MI:0914”(association)	0.530
LGALS3	PODXL	psi-mi:“MI:0914”(association)	0.530
CHRNA9	CHEK1	psi-mi:“MI:0914”(association)	0.530
CLGN	NPC1	psi-mi:“MI:0914”(association)	0.530
PTGIR	TMEM63A	psi-mi:“MI:0914”(association)	0.530
CSGALNACT2	TPST1	psi-mi:“MI:0914”(association)	0.530
DIRAS3	DCAF10	psi-mi:“MI:0914”(association)	0.530
GALNT16	IPO8	psi-mi:“MI:0914”(association)	0.530
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530
TMEM9	ESYT2	psi-mi:“MI:0914”(association)	0.530
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
TMEM163	SLC30A1	psi-mi:“MI:0915”(physical association)	0.460
TMEM163	SLC30A1	psi-mi:“MI:0403”(colocalization)	0.460

BioGRID (257): SLC30A1 (Affinity Capture-MS), SLC30A1 (Affinity Capture-MS), SLC30A1 (Affinity Capture-MS), SLC30A1 (Affinity Capture-MS), SLC30A1 (Affinity Capture-MS), SLC30A1 (Affinity Capture-MS), SLC30A1 (Proximity Label-MS), SLC30A1 (Affinity Capture-MS), SLC30A1 (Proximity Label-MS), SLC30A1 (Proximity Label-MS), SLC30A1 (Affinity Capture-MS), SLC30A1 (Affinity Capture-MS), SLC30A1 (Affinity Capture-MS), SLC30A1 (Affinity Capture-MS), SLC30A1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2KQY6, A4IFD7, A5D7L5, A5PMX1, O13918, O14863, O35149, O45923, O55174, P0CE46, P20107, P32798, P97441, Q08E25, Q15043, Q28CE7, Q2HJ10, Q3UVU3, Q4R6K2, Q52KD7, Q5BJM8, Q5FVQ0, Q5I020, Q5MNV6, Q5R617, Q5RAB7, Q5XHB4, Q5ZLF4, Q60738, Q62720, Q62941, Q6DBM8, Q6DG36, Q6NRI1, Q6P3N9, Q6QIX3, Q6XR72, Q75N73, Q8BGG0, Q8H329

Diamond homologs: A5PMX1, O13918, P20107, P30540, P32798, Q3UVU3, Q4R6K2, Q54F34, Q5MNV6, Q60738, Q62720, Q6AZN8, Q6DG36, Q6P0D1, Q6XR72, Q9Y6M5, P9WGF4, P9WGF5, Q03455, Q08970, Q28CE7, Q5BJM8, Q5I020, Q5XHB4, Q5ZLF4, Q6ICY4, Q8H329, Q8NEW0, Q9BRI3, Q9JKN1, A4IFD7, A7Z1S6, O07084, O14863, O35149, O45923, O55174, P0CE46, P13512, P55237

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 139 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
GRB2 events in EGFR signaling	5	39.6×	4e-05
SHC1 events in EGFR signaling	5	37.2×	4e-05
Signaling by SCF-KIT	5	12.9×	1e-03
Neutrophil degranulation	13	3.1×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
monoatomic ion transmembrane transport	6	10.1×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	28
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

205 predictions. Top by Δscore:

Variant	Effect	Δscore
1:211576290:C:CC	acceptor_gain	1.0000
1:211577980:T:A	donor_gain	1.0000
1:211576122:C:CT	donor_gain	0.9900
1:211576123:T:TT	donor_gain	0.9900
1:211576123:TAC:T	donor_gain	0.9900
1:211576125:C:CT	donor_gain	0.9900
1:211576126:T:TT	donor_gain	0.9900
1:211576171:TC:T	donor_gain	0.9900
1:211576172:C:CA	donor_gain	0.9900
1:211576172:CC:C	donor_gain	0.9900
1:211576199:T:C	donor_gain	0.9900
1:211576205:T:TA	donor_gain	0.9900
1:211576285:TGGGT:T	acceptor_gain	0.9900
1:211576286:GGGT:G	acceptor_gain	0.9900
1:211576286:GGGTC:G	acceptor_gain	0.9900
1:211576287:GGT:G	acceptor_gain	0.9900
1:211576288:GT:G	acceptor_gain	0.9900
1:211576289:TC:T	acceptor_loss	0.9900
1:211576290:C:CG	acceptor_loss	0.9900
1:211576291:T:G	acceptor_loss	0.9900
1:211577987:TCACC:T	donor_loss	0.9900
1:211577988:CACCT:C	donor_loss	0.9900
1:211577989:A:C	donor_loss	0.9900
1:211577990:C:CA	donor_loss	0.9900
1:211576118:T:C	donor_gain	0.9800
1:211576287:GGTCT:G	acceptor_gain	0.9800
1:211576288:GTCT:G	acceptor_gain	0.9800
1:211576289:TCT:T	acceptor_gain	0.9800
1:211577990:CCTG:C	donor_gain	0.9800
1:211576122:CTA:C	donor_gain	0.9700

AlphaMissense

3321 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:211575649:A:C	F421L	1.000
1:211575649:A:T	F421L	1.000
1:211575650:A:G	F421S	1.000
1:211575651:A:G	F421L	1.000
1:211575713:G:T	A400D	1.000
1:211575749:A:T	I388K	1.000
1:211575755:G:T	A386D	1.000
1:211575756:C:G	A386P	1.000
1:211575761:G:T	A384D	1.000
1:211575762:C:G	A384P	1.000
1:211575782:A:G	L377P	1.000
1:211575787:C:A	W375C	1.000
1:211575787:C:G	W375C	1.000
1:211575789:A:G	W375R	1.000
1:211575789:A:T	W375R	1.000
1:211575791:A:T	V374D	1.000
1:211575833:A:G	L360P	1.000
1:211575869:G:T	P348H	1.000
1:211575881:A:G	L344P	1.000
1:211575884:A:G	L343P	1.000
1:211575905:A:G	L336P	1.000
1:211576148:T:A	D255V	1.000
1:211576148:T:G	D255A	1.000
1:211578358:G:C	N85K	1.000
1:211578358:G:T	N85K	1.000
1:211578365:A:G	L83P	1.000
1:211578371:C:T	G81E	1.000
1:211578372:C:G	G81R	1.000
1:211578372:C:T	G81R	1.000
1:211578395:C:A	G73V	1.000

dbSNP variants (sampled 300 via entrez): RS1000008441 (1:211579219 C>A,T), RS1000267755 (1:211579035 C>A), RS1000724072 (1:211578745 C>G,T), RS1000856248 (1:211571707 AAC>A), RS1001366416 (1:211579363 C>T), RS1001530888 (1:211574988 A>T), RS1001995607 (1:211576705 T>C), RS1002147593 (1:211573837 G>A,C), RS1002266418 (1:211573446 G>A,T), RS1002632237 (1:211572581 G>A), RS1002802697 (1:211577698 T>C), RS1003030576 (1:211572993 C>T), RS1004299963 (1:211571169 A>G), RS1004788367 (1:211579369 G>A,T), RS1004840845 (1:211579129 G>A)

Disease associations

OMIM: gene MIM:609521 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST000973_7	Hypertension	1.000000e-06
GCST012106_1	Nevus count	2.000000e-08
GCST90000025_845	Appendicular lean mass	6.000000e-18
GCST90011900_29	Serum alkaline phosphatase levels	2.000000e-12

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004632	nevus count
EFO:0004980	appendicular lean mass
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC30 zinc transporter family

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Zinc	increases transport, increases uptake, affects cotreatment, increases expression, decreases expression (+3 more)	15
sodium arsenite	affects methylation, affects cotreatment, increases expression, decreases expression, increases abundance	11
Cadmium Chloride	increases palmitoylation, increases expression, decreases reaction, increases abundance	9
Cadmium	affects localization, decreases reaction, increases abundance, increases palmitoylation, increases expression	8
Zinc Sulfate	increases expression, increases reaction, decreases reaction	8
Valproic Acid	increases expression, affects expression, affects cotreatment	6
zinc chloride	decreases reaction, increases expression, decreases expression	4
Arsenic Trioxide	increases expression, affects response to substance	4
Cisplatin	affects expression, decreases response to substance, increases expression	4
bisphenol A	affects expression, increases expression	3
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediamine	affects cotreatment, decreases reaction, increases expression, decreases expression, increases reaction	3
Benzo(a)pyrene	affects methylation, increases expression	3
Genistein	affects expression, increases expression	3
cobaltous chloride	affects expression, increases expression	2
perfluorooctanoic acid	decreases expression, increases expression	2
cupric oxide	increases expression	2
mercuric bromide	increases expression, affects cotreatment	2
epigallocatechin gallate	decreases reaction, increases expression, decreases expression, affects cotreatment	2
motexafin gadolinium	affects reaction, increases expression, affects cotreatment	2
Acetaminophen	decreases expression, increases expression	2
Copper	decreases expression, increases expression, affects binding	2
Estradiol	increases expression	2
Ethinyl Estradiol	affects expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Rotenone	increases expression	2
Silver	increases expression	2
Aflatoxin B1	decreases methylation, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
Particulate Matter	increases abundance, increases expression, affects cotreatment	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B2FV	Abcam HeLa SLC30A1 KO	Cancer cell line	Female
CVCL_D4LA	HCT116-SLC30A1-KO-c3	Cancer cell line	Male
CVCL_D4LB	HCT116-SLC30A1-KO-c4	Cancer cell line	Male
CVCL_TM86	HAP1 SLC30A1 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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