SLC39A1

Summary

SLC39A1 (solute carrier family 39 member 1, HGNC:12876) is a protein-coding gene on chromosome 1q21.3, encoding Zinc transporter ZIP1 (Q9NY26). Transporter for the divalent cation Zn(2+).

This gene encodes a member of the zinc-iron permease family. The encoded protein is localized to the cell membrane and acts as a zinc uptake transporter. This gene has been linked to prostate cancer, breast cancer, and Alzheimer’s disease. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 27173 — RefSeq curated summary.

At a glance

• GWAS associations: 18
• Clinical variants (ClinVar): 45 total
• MANE Select transcript: NM_001271958

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12876
Approved symbol	SLC39A1
Name	solute carrier family 39 member 1
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Aliases	ZIP1
Ensembl gene	ENSG00000143570
Ensembl biotype	protein_coding
OMIM	604740
Entrez	27173

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 24 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000310483, ENST00000356205, ENST00000368621, ENST00000368623, ENST00000413622, ENST00000417348, ENST00000461071, ENST00000537590, ENST00000617697, ENST00000621013, ENST00000885397, ENST00000885398, ENST00000885399, ENST00000885400, ENST00000885401, ENST00000930165, ENST00000930166, ENST00000930167, ENST00000930168, ENST00000930169, ENST00000930170, ENST00000930171, ENST00000945941, ENST00000945942, ENST00000945943

RefSeq mRNA: 6 — MANE Select: NM_001271958 NM_001271957, NM_001271958, NM_001271959, NM_001271960, NM_001271961, NM_014437

CCDS: CCDS1055, CCDS72920

Canonical transcript exons

ENST00000356205 — 4 exons

Exon	Start	End
ENSE00000960933	153962220	153962350
ENSE00001447602	153963495	153963537
ENSE00001551779	153959110	153960754
ENSE00003754499	153962529	153962747

Expression profiles

Bgee: expression breadth ubiquitous, 141 present calls, max score 98.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.7386 / max 142.2486, expressed in 1818 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
14751	33.4195	1815
14749	2.3010	1348
14750	1.0703	627
14745	0.9909	534
14753	0.9276	536
14746	0.3070	155
14747	0.2749	139
14748	0.2381	93
14752	0.2093	110

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
placenta	UBERON:0001987	98.00	gold quality
calcaneal tendon	UBERON:0003701	97.97	gold quality
upper lobe of left lung	UBERON:0008952	96.57	gold quality
metanephros cortex	UBERON:0010533	96.33	gold quality
stromal cell of endometrium	CL:0002255	96.07	gold quality
right lung	UBERON:0002167	96.07	gold quality
gall bladder	UBERON:0002110	96.05	gold quality
right adrenal gland	UBERON:0001233	96.03	gold quality
left adrenal gland	UBERON:0001234	96.03	gold quality
descending thoracic aorta	UBERON:0002345	95.99	gold quality
thoracic aorta	UBERON:0001515	95.95	gold quality
ascending aorta	UBERON:0001496	95.90	gold quality
left adrenal gland cortex	UBERON:0035825	95.87	gold quality
right coronary artery	UBERON:0001625	95.86	gold quality
right adrenal gland cortex	UBERON:0035827	95.83	gold quality
islet of Langerhans	UBERON:0000006	95.75	gold quality
mucosa of stomach	UBERON:0001199	95.49	gold quality
adult mammalian kidney	UBERON:0000082	95.38	gold quality
lung	UBERON:0002048	95.28	gold quality
left coronary artery	UBERON:0001626	95.24	gold quality
subcutaneous adipose tissue	UBERON:0002190	95.24	gold quality
adrenal gland	UBERON:0002369	95.22	gold quality
adipose tissue	UBERON:0001013	95.21	gold quality
omental fat pad	UBERON:0010414	95.18	gold quality
right lobe of thyroid gland	UBERON:0001119	95.17	gold quality
left uterine tube	UBERON:0001303	95.01	gold quality
body of stomach	UBERON:0001161	94.98	gold quality
skin of leg	UBERON:0001511	94.94	gold quality
endocervix	UBERON:0000458	94.91	gold quality
myometrium	UBERON:0001296	94.77	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.49
E-MTAB-6678	yes	6.21
E-GEOD-100618	no	264.46

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CREB1, RREB1, SP1

miRNA regulators (miRDB)

56 targeting SLC39A1, 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-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-5683	99.36	68.59	2083
HSA-MIR-133A-3P	99.27	71.53	1270
HSA-MIR-133B	99.27	71.53	1270

Literature-anchored findings (GeneRIF, showing 24)

• zip1 mechanism of transport appears to involve the transport of zinc from low molecular weight ligands that exist in circulation as relatively loosely bound complexes with zinc (PMID:12888280)
• ZIP1, ZIP2 and ZIP3 may play cell-specific roles in zinc homeostasis rather than primary roles in the acquisition of dietary zinc (PMID:14525987)
• down regulation of hZIP1 is a critical early event in the development prostate cancer (PMID:16153295)
• In conclusion, these studies provide important insights into the role of a plasma membrane zinc transporter (ZIP1) in the initiation of an osteogenic lineage from MSCs. (PMID:16203195)
• di-leucine sorting signal of ZIP1 was required and sufficient for endocytosis of the chimeric proteins (PMID:17635580)
• Gene expression regulation of ZIPs after zinc supplementation. (PMID:18279033)
• results show that hZIP1 overexpression has a functional effect on the malignant potential of prostate cancer cells via inhibition of NF-kappaB-dependent pathways and support the concept that hZIP1 may function as a tumor suppressor gene (PMID:18765529)
• The core promoter region responsible for constitutive expression of hZip1 were identified and critical roles for SP1 and CREB1 in transcriptional regulation of the hZip1 gene in prostate cancer cells, was demonstrated. (PMID:19026724)
• ZIP is a novel transcription repressor, represses EGFR oncogene and suppresses breast carcinogenesis (PMID:19644445)
• Ras pathway and activation of RREB-1 are involved in hZIP1 down-regulation and may play a role in the decrease of the transporter expression in prostate cancer. (PMID:19802870)
• GSPE and EGCG enhance the expression of cellular zinc importers ZIP1 (SLC39A1). (PMID:20471814)
• the expression of human Zn transporter1 (hZIP1) appears to correlate with the Zn levels in the prostate glands and may be the major Zn regulator in this organ. (PMID:20705137)
• 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)
• RREB-1 overexpression results in down-regulation of hZIP1 and contributes to the loss of hZIP1 expression and zinc in prostate cancer. (PMID:21360563)
• 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)
• 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 the average expression level of zinc transporter Zip2 was significantly higher and zinc transporters Zip6, Zip8 mRNA levels were significantly lower in short stature children than in health controls. (PMID:23921484)
• Data indicate that zinc transporters ZnT1 and Zip1 were the most abundantly expressed zinc transporters in leukocytes. (PMID:24488210)
• Data suggest that high zrt- and Irt-like protein 1 (hZIP1) expression may be an indicator of good prognosis in clear cell renal cell carcinoma (ccRCC). (PMID:24878177)
• The effect of zinc administered for 27 days on the expression of ZIP1 in peripheral white blood cells is reported. (PMID:24922175)
• Despite the fact that these preliminary findings are unlikely to be of much diagnostic significance, these findings suggest that hZip1 plays a fundamental role in the carcinogenesis of mucinous tumors. (PMID:26081940)
• Mitochondrial membrane potential is reduced focally at a fission site by the Drp1 recruitment, which is initiated by the interaction of Drp1 with mitochondrial zinc transporter Zip1 and Zn(2+) entry through the Zip1-MCU complex. After division, healthy mitochondria restore MMP levels and participate in the fusion-fission cycle again, but mitochondria that fail to restore MMP undergo mitophagy. (PMID:30581142)
• Decreased SLC39A1 (Solute carrier family 39 member 1) expression predicts unfavorable prognosis in patients with early-stage hepatocellular carcinoma. (PMID:34615436)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Slc39a1	ENSMUSG00000052310
rattus_norvegicus	Slc39a1	ENSRNOG00000059463
caenorhabditis_elegans		WBGENE00014669
caenorhabditis_elegans		WBGENE00017936

Paralogs (2): SLC39A3 (ENSG00000141873), SLC39A2 (ENSG00000165794)

Protein

Protein identifiers

Zinc transporter ZIP1 — Q9NY26 (reviewed: Q9NY26)

Alternative names: Solute carrier family 39 member 1, Zinc-iron-regulated transporter-like, Zrt- and Irt-like protein 1

All UniProt accessions (4): Q9NY26, A0A0A0MTL8, Q5T4K2, Q5T4K4

UniProt curated annotations — full annotation on UniProt →

Function. Transporter for the divalent cation Zn(2+). Mediates the influx of Zn(2+) into cells from extracellular space. Functions as the major importer of zinc from circulating blood plasma into prostate cells.

Subcellular location. Cell membrane. Endoplasmic reticulum membrane.

Tissue specificity. Ubiquitous. Expressed in most adult and fetal tissues including the epidermis.

Activity regulation. Inhibited by Ni(2+) ions. Fe(2+) ions do not inhibit zinc uptake.

Induction. Down-regulated in prostate cancer.

Miscellaneous. Inhibited by Ni(2+) ions. Fe(2+) ions do not inhibit zinc uptake.

Similarity. Belongs to the ZIP transporter (TC 2.A.5) family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NY26-1	1	yes
Q9NY26-2	2

RefSeq proteins (6): NP_001258886, NP_001258887, NP_001258888, NP_001258889, NP_001258890, NP_055252 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003689	ZIP	Family

Pfam: PF02535

Catalyzed reactions (Rhea), 1 shown:

• Zn(2+)(in) = Zn(2+)(out) (RHEA:29351)

UniProt features (28 total): topological domain 8, transmembrane region 8, sequence conflict 6, mutagenesis site 4, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NY26-F1	80.51	0.43

Functional residue map

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

Mutagenesis-validated functional residues (4):

Position	Phenotype
158	does not affect membrane localization; when associated with a-160. decreases zinc uptake; when associated with a-160.
160	does not affect membrane localization; when associated with a-158. decreases zinc uptake; when associated with a-158.
190	does not affect membrane localization. decreases zinc uptake.
217	does not affect membrane localization. decreases zinc uptake.

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

ID	Pathway
R-HSA-442380	Zinc influx into cells by the SLC39 gene family
R-HSA-382551	Transport of small molecules
R-HSA-425366
R-HSA-425407	SLC-mediated transmembrane transport
R-HSA-425410	Metal ion SLC transporters
R-HSA-435354	Zinc transporters

MSigDB gene sets: 177 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, MULLIGHAN_NPM1_SIGNATURE_3_UP, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_TRANSITION_METAL_ION_TRANSPORT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_MORPHOGENESIS, GOBP_MONOATOMIC_CATION_TRANSPORT, PATIL_LIVER_CANCER, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, GOBP_EMBRYONIC_ORGAN_MORPHOGENESIS, GOBP_APPENDAGE_DEVELOPMENT, GOBP_CRANIAL_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYO_DEVELOPMENT, GOMF_SIGNALING_RECEPTOR_BINDING

GO Biological Process (9): in utero embryonic development (GO:0001701), monoatomic cation transport (GO:0006812), embryonic cranial skeleton morphogenesis (GO:0048701), limb development (GO:0060173), zinc ion transmembrane transport (GO:0071577), monoatomic ion transport (GO:0006811), zinc ion transport (GO:0006829), metal ion transport (GO:0030001), transmembrane transport (GO:0055085)

GO Molecular Function (5): signaling receptor binding (GO:0005102), zinc ion transmembrane transporter activity (GO:0005385), obsolete inorganic cation transmembrane transporter activity (GO:0022890), protein binding (GO:0005515), metal ion transmembrane transporter activity (GO:0046873)

GO Cellular Component (4): endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), membrane (GO:0016020), endoplasmic reticulum (GO:0005783)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Zinc transporters	1
Transport of small molecules	1
SLC-mediated transmembrane transport	1
Metal ion SLC transporters	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	2
chordate embryonic development	1
monoatomic ion transport	1
embryonic skeletal system morphogenesis	1
cranial skeletal system development	1
appendage development	1
zinc ion transport	1
monoatomic cation transmembrane transport	1
transition metal ion transport	1
monoatomic cation transport	1
cellular process	1
protein binding	1
transition metal ion transmembrane transporter activity	1
zinc ion transmembrane transport	1
binding	1
monoatomic cation transmembrane transporter activity	1
metal ion transport	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
membrane	1
cell periphery	1
cellular anatomical structure	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

998 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC39A1	SLC30A1	Q9Y6M5	893
SLC39A1	SLC30A4	O14863	867
SLC39A1	HFM1	A2PYH4	849
SLC39A1	SPO11	Q9Y5K1	838
SLC39A1	SLC11A2	P49281	836
SLC39A1	SLC40A1	Q9NP59	832
SLC39A1	MSH4	O15457	822
SLC39A1	C1orf146	Q5VVC0	821
SLC39A1	SLC39A7	Q92504	821
SLC39A1	SLC39A9	Q9NUM3	814
SLC39A1	SLC30A5	Q8TAD4	797
SLC39A1	SLC39A6	Q13433	795
SLC39A1	SLC39A14	Q15043	794
SLC39A1	SLC39A10	Q9ULF5	794
SLC39A1	SLC30A7	Q8NEW0	792

IntAct

56 interactions, top by confidence:

A	B	Type	Score
SLC39A1	NME2P1	psi-mi:“MI:0914”(association)	0.560
TMEM60	SLC39A1	psi-mi:“MI:0915”(physical association)	0.560
TUSC5	SLC39A1	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	SLC39A1	psi-mi:“MI:0915”(physical association)	0.560
CXCL16	SLC39A1	psi-mi:“MI:0915”(physical association)	0.560
COMT	SLC39A1	psi-mi:“MI:0915”(physical association)	0.560
CYB561	SLC39A1	psi-mi:“MI:0915”(physical association)	0.560
CXCL9	SLC39A1	psi-mi:“MI:0915”(physical association)	0.560
SLC39A1	OPTN	psi-mi:“MI:0915”(physical association)	0.560
SLC39A1	NME2P1	psi-mi:“MI:0915”(physical association)	0.560
SLC39A1	HTR2C	psi-mi:“MI:0915”(physical association)	0.550
SLC7A1	TMEM223	psi-mi:“MI:0914”(association)	0.530
C3AR1	TMEM120B	psi-mi:“MI:0914”(association)	0.530
HTR2C	KLRG2	psi-mi:“MI:0914”(association)	0.530
ADGRG5	KLRG2	psi-mi:“MI:0914”(association)	0.530
PTGER3	PIK3R2	psi-mi:“MI:0914”(association)	0.530
FCGRT	GOLIM4	psi-mi:“MI:0914”(association)	0.530
FZD10	NRP1	psi-mi:“MI:0914”(association)	0.530
SPPL2B	UQCRQ	psi-mi:“MI:0914”(association)	0.530
SLC39A1	SORBS3	psi-mi:“MI:0915”(physical association)	0.400
SLC39A1	HTR4	psi-mi:“MI:0915”(physical association)	0.370
SLC39A1	CERS2	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (75): SLC39A1 (Affinity Capture-RNA), SLC39A1 (Affinity Capture-RNA), SLC39A1 (Reconstituted Complex), LSG1 (Affinity Capture-MS), SUPT6H (Affinity Capture-MS), SLC39A1 (Affinity Capture-MS), SLC39A1 (Affinity Capture-MS), SLC39A1 (Affinity Capture-MS), SLC39A1 (Affinity Capture-MS), SLC39A1 (Affinity Capture-MS), SLC39A1 (Affinity Capture-MS), SLC39A1 (Affinity Capture-MS), SLC39A1 (Affinity Capture-MS), SLC39A1 (Affinity Capture-MS), SLC39A1 (Affinity Capture-MS)

ESM2 similar proteins: A6NGC4, A6NKX4, A6NM10, F1NZP5, O96011, P0C242, P27544, P27545, Q0VCY6, Q2TBI8, Q3SYU3, Q4V8E5, Q5F2F2, Q5JZQ7, Q5RFI0, Q5U2T1, Q5U419, Q6AYM9, Q6GQT6, Q6PIS1, Q6TCG5, Q6UXD7, Q6UXT9, Q71RH2, Q7TNV1, Q7Z403, Q80ZE4, Q863Y8, Q86WI3, Q8BMT9, Q8CHK3, Q8IU68, Q8IXF9, Q8N9H8, Q8TBR7, Q8VC26, Q8WUG5, Q96N66, Q99640, Q99JT6

Diamond homologs: G3X943, P59889, Q3SYU3, Q55EA1, Q6QQT1, Q9BRY0, Q9NP94, Q9NY26, Q9QZ03, Q54MB9, Q5E960, Q5U1X7, Q99K24, C6KST8, A4IIC5, Q852F6, Q94DG6, Q9LTH9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 46 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
G alpha (i) signalling events	7	9.1×	1e-03

GO biological processes:

GO term	Partners	Fold	FDR
phospholipase C-activating G protein-coupled receptor signaling pathway	6	21.4×	1e-04
chemotaxis	5	18.4×	9e-04
adenylate cyclase-activating G protein-coupled receptor signaling pathway	5	15.3×	2e-03
G protein-coupled receptor signaling pathway	7	6.9×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	41
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

673 predictions. Top by Δscore:

Variant	Effect	Δscore
1:153962218:A:AC	donor_gain	1.0000
1:153962219:C:CC	donor_gain	1.0000
1:153962351:C:CC	acceptor_gain	1.0000
1:153962524:CTTA:C	donor_loss	1.0000
1:153962525:TTAC:T	donor_loss	1.0000
1:153962526:TA:T	donor_loss	1.0000
1:153962527:A:AC	donor_gain	1.0000
1:153962527:AC:A	donor_gain	1.0000
1:153962527:ACCT:A	donor_loss	1.0000
1:153962528:C:CA	donor_gain	1.0000
1:153962528:CC:C	donor_gain	1.0000
1:153962528:CCTG:C	donor_gain	1.0000
1:153962528:CCTGA:C	donor_gain	1.0000
1:153960750:TGGAG:T	acceptor_gain	0.9900
1:153960752:GAGCT:G	acceptor_loss	0.9900
1:153960755:C:A	acceptor_loss	0.9900
1:153960755:C:CC	acceptor_gain	0.9900
1:153960756:T:A	acceptor_loss	0.9900
1:153960772:A:T	acceptor_gain	0.9900
1:153960783:C:CT	acceptor_gain	0.9900
1:153962214:GCTCA:G	donor_loss	0.9900
1:153962215:CT:C	donor_loss	0.9900
1:153962216:TCA:T	donor_loss	0.9900
1:153962217:CA:C	donor_loss	0.9900
1:153962218:A:AG	donor_loss	0.9900
1:153962219:C:CA	donor_loss	0.9900
1:153962219:CCG:C	donor_gain	0.9900
1:153962219:CCGT:C	donor_gain	0.9900
1:153962346:GGAAG:G	acceptor_gain	0.9900
1:153962347:GAAG:G	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000069787 (1:153967407 G>C), RS1000101967 (1:153967761 G>A), RS1000906345 (1:153962801 A>C), RS1001142587 (1:153966841 T>C), RS1001172019 (1:153967289 C>G), RS1001193282 (1:153967887 C>G,T), RS1001340838 (1:153961725 A>G), RS1001855589 (1:153961995 G>T), RS1002700948 (1:153958803 G>A), RS1002848754 (1:153965533 A>C), RS1003120918 (1:153963527 G>A,C), RS1003183682 (1:153964264 C>T), RS1003417651 (1:153963167 C>A,T), RS1003863840 (1:153964675 G>C), RS1004131770 (1:153963576 T>C)

Disease associations

OMIM: gene MIM:604740 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

18 associations (top):

Study	Trait	p-value
GCST001640_10	Lentiform nucleus volume	4.000000e-06
GCST003795_1	Age at first birth	6.000000e-10
GCST005751_3	Empathy quotient	3.000000e-07
GCST006044_1	Age at first birth	3.000000e-07
GCST006045_3	Age at first birth	5.000000e-06
GCST010136_18	Fruit consumption	3.000000e-08
GCST010137_3	Cooked vegetable consumption	3.000000e-09
GCST010138_14	Raw vegetable consumption	5.000000e-11
GCST010142_60	Fish- and plant-related diet	4.000000e-09
GCST010142_92	Fish- and plant-related diet	6.000000e-14
GCST010696_22	Cortical thickness (min-P)	4.000000e-10
GCST010697_50	Cortical surface area (min-P)	1.000000e-12
GCST010698_81	Subcortical volume (min-P)	1.000000e-23
GCST010699_7	Brain morphology (min-P)	1.000000e-10
GCST010700_11	Cortical thickness (MOSTest)	4.000000e-13
GCST010701_73	Cortical surface area (MOSTest)	4.000000e-09
GCST010702_45	Subcortical volume (MOSTest)	4.000000e-10
GCST010703_276	Brain morphology (MOSTest)	2.000000e-15

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0009101	age at first birth measurement
EFO:0009183	empathy measurement
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness

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 — SLC39 family of metal ion transporters

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Zinc	decreases expression, increases reaction, increases transport, increases uptake	5
Benzo(a)pyrene	increases expression, increases methylation	3
Aflatoxin B1	affects expression, increases expression	2
Zinc Sulfate	increases expression, decreases expression	2
aristolochic acid I	increases expression	1
bufotalin	increases expression	1
beta-lapachone	increases expression	1
zinc chloride	increases expression, decreases reaction	1
cobaltous chloride	decreases expression	1
ochratoxin A	decreases expression, increases reaction	1
diallyl trisulfide	decreases expression	1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediamine	increases expression	1
epigallocatechin gallate	increases expression	1
monomethylarsonous acid	increases expression	1
ICG 001	decreases expression	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	decreases reaction, increases expression	1
Cadmium	decreases expression	1
Calcitriol	decreases expression	1
Cisplatin	decreases response to substance, increases expression	1
Environmental Pollutants	affects expression	1
Selenium	affects cotreatment, increases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1
Vanadium	decreases expression	1
Vitamin E	affects cotreatment, increases expression	1
Cadmium Chloride	increases expression	1

Cellosaurus cell lines

6 cell lines: 6 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2G5	Abcam HeLa SLC39A1 KO	Cancer cell line	Female
CVCL_D4NA	HCT116-SLC39A1-KO-c10	Cancer cell line	Male
CVCL_D4NB	HCT116-SLC39A1-KO-c8	Cancer cell line	Male
CVCL_D6BU	HyCyte Huh-7 KO-hSLC39A1	Cancer cell line	Male
CVCL_TN50	HAP1 SLC39A1 (-) 1	Cancer cell line	Male
CVCL_TN51	HAP1 SLC39A1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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