SLC30A9

Summary

SLC30A9 (solute carrier family 30 member 9, HGNC:1329) is a protein-coding gene on chromosome 4p13, encoding Proton-coupled zinc antiporter SLC30A9, mitochondrial (Q6PML9). Mitochondrial proton-coupled zinc ion antiporter mediating the export of zinc from the mitochondria and involved in zinc homeostasis, zinc mobilization as well as mitochondrial morphology and health. It is a selective cancer dependency (DepMap: 15.4% of cell lines).

Enables zinc ion transmembrane transporter activity. Involved in intracellular zinc ion homeostasis; regulation of mitochondrion organization; and zinc ion transport. Located in several cellular components, including cytoplasmic vesicle; endoplasmic reticulum; and mitochondrial membrane.

Source: NCBI Gene 10463 — RefSeq curated summary.

At a glance

• Gene–disease (curated): psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome (Definitive, ClinGen)
• GWAS associations: 6
• Clinical variants (ClinVar): 101 total — 2 pathogenic, 3 likely-pathogenic
• Phenotypes (HPO): 44
• Cancer dependency (DepMap): dependent in 15.4% of screened cell lines
• MANE Select transcript: NM_006345

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1329
Approved symbol	SLC30A9
Name	solute carrier family 30 member 9
Location	4p13
Locus type	gene with protein product
Status	Approved
Aliases	HUEL, ZNT9, GAC63
Ensembl gene	ENSG00000014824
Ensembl biotype	protein_coding
OMIM	604604
Entrez	10463

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 13 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000264451, ENST00000505523, ENST00000509683, ENST00000510460, ENST00000513699, ENST00000866307, ENST00000866308, ENST00000866309, ENST00000866310, ENST00000866311, ENST00000866312, ENST00000866313, ENST00000866314, ENST00000866315, ENST00000962777, ENST00000962778, ENST00000962779

RefSeq mRNA: 1 — MANE Select: NM_006345 NM_006345

CCDS: CCDS3465

Canonical transcript exons

ENST00000264451 — 18 exons

Exon	Start	End
ENSE00001145169	42086082	42090461
ENSE00002023549	41990530	41990760
ENSE00003472801	42070526	42070691
ENSE00003474429	42018111	42018170
ENSE00003482057	42062986	42063121
ENSE00003486941	42049377	42049479
ENSE00003505783	42066550	42066621
ENSE00003517552	42038986	42039053
ENSE00003523855	42020416	42020515
ENSE00003548916	42060191	42060246
ENSE00003618797	42022838	42022930
ENSE00003620875	42035275	42035333
ENSE00003656620	42001616	42001780
ENSE00003658770	42075657	42075786
ENSE00003662465	42078212	42078325
ENSE00003675561	42023302	42023384
ENSE00003692324	42067085	42067192
ENSE00003694318	42065310	42065349

Expression profiles

Bgee: expression breadth ubiquitous, 300 present calls, max score 97.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 64.7474 / max 775.0952, expressed in 1823 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
47509	61.3961	1820
47510	3.3513	1450

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	97.11	gold quality
calcaneal tendon	UBERON:0003701	96.76	gold quality
germinal epithelium of ovary	UBERON:0001304	96.64	gold quality
adrenal tissue	UBERON:0018303	96.62	gold quality
nephron tubule	UBERON:0001231	96.58	gold quality
tibia	UBERON:0000979	96.52	gold quality
ganglionic eminence	UBERON:0004023	96.21	gold quality
ventricular zone	UBERON:0003053	96.02	gold quality
epithelium of nasopharynx	UBERON:0001951	95.87	gold quality
nasopharynx	UBERON:0001728	95.85	gold quality
middle temporal gyrus	UBERON:0002771	95.84	gold quality
pigmented layer of retina	UBERON:0001782	95.53	gold quality
postcentral gyrus	UBERON:0002581	95.46	gold quality
tendon	UBERON:0000043	95.39	gold quality
medial globus pallidus	UBERON:0002477	95.26	gold quality
prefrontal cortex	UBERON:0000451	95.22	gold quality
eye	UBERON:0000970	95.14	gold quality
corpus epididymis	UBERON:0004359	95.12	gold quality
palpebral conjunctiva	UBERON:0001812	95.04	gold quality
rectum	UBERON:0001052	94.97	gold quality
superior frontal gyrus	UBERON:0002661	94.97	gold quality
mucosa of sigmoid colon	UBERON:0004993	94.94	gold quality
Brodmann (1909) area 23	UBERON:0013554	94.75	gold quality
parietal lobe	UBERON:0001872	94.73	gold quality
heart right ventricle	UBERON:0002080	94.67	gold quality
orbitofrontal cortex	UBERON:0004167	94.65	gold quality
globus pallidus	UBERON:0001875	94.61	gold quality
caput epididymis	UBERON:0004358	94.57	gold quality
corpus callosum	UBERON:0002336	94.45	gold quality
renal glomerulus	UBERON:0000074	94.43	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.35

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

115 targeting SLC30A9, 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-340-5P	100.00	72.50	4437
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-548AE-3P	99.93	72.66	4867

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 15.4% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 11)

• Results indicate that HUEL, which shares significant homology with the DNA-binding domain of XPA, is likely to be a conserved, housekeeping gene that is intimately linked with cellular replication, DNA synthesis and/or transcriptional regulation. (PMID:11906820)
• hZnT-9 was expressed at low levels in leukocytes. (PMID:17971500)
• ZNT9 expression in glioma tumors was not associated with tumor grade or IDH1 mutation status. (PMID:25921144)
• SLC30A9 has zinc transport properties affecting intracellular zinc homeostasis, and that the molecular mechanism of the disease is through defective function of this novel activity of SLC30A9 (PMID:28334855)
• Expression of zinc transporters ZIP4, ZIP14 and ZnT9 in hepatic carcinogenesis-An immunohistochemical study (PMID:29895370)
• Genetic Variants May Play Role in Opioid Dependence. (PMID:32453508)
• Zinc Transporter 9 (SLC30A9) Expression Is Decreased in the Vaginal Tissues of Menopausal Women. (PMID:33409913)
• SLC-30A9 is required for Zn(2+) homeostasis, Zn(2+) mobilization, and mitochondrial health. (PMID:34433664)
• Clinical Phenotype in Individuals With Birk-Landau-Perez Syndrome Associated With Biallelic SLC30A9 Pathogenic Variants. (PMID:37041080)
• N-acetyltransferase 10 facilitates tumorigenesis of diffuse large B-cell lymphoma by regulating AMPK/mTOR signalling through N4-acetylcytidine modification of SLC30A9. (PMID:38961519)
• SLC30A9: an evolutionarily conserved mitochondrial zinc transporter essential for mammalian early embryonic development. (PMID:39158587)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc30a9	ENSDARG00000057272
mus_musculus	Slc30a9	ENSMUSG00000029221
rattus_norvegicus	Slc30a9	ENSRNOG00000002246
drosophila_melanogaster	ZnT49B	FBGN0033762
caenorhabditis_elegans		WBGENE00022174

Protein

Protein identifiers

Proton-coupled zinc antiporter SLC30A9, mitochondrial — Q6PML9 (reviewed: Q6PML9)

Alternative names: Human embryonic lung protein, Solute carrier family 30 member 9, Zinc transporter 9

All UniProt accessions (3): Q6PML9, A0A0S2Z514, D6R9M6

UniProt curated annotations — full annotation on UniProt →

Function. Mitochondrial proton-coupled zinc ion antiporter mediating the export of zinc from the mitochondria and involved in zinc homeostasis, zinc mobilization as well as mitochondrial morphology and health. In nucleus, functions as a secondary coactivator for nuclear receptors by cooperating with p160 coactivators subtypes. Plays a role in transcriptional activation of Wnt-responsive genes.

Subunit / interactions. Interacts with GRIP1, ESR1 and AR.

Subcellular location. Mitochondrion membrane. Nucleus. Endoplasmic reticulum.

Tissue specificity. Ubiquitously expressed in fetal and adult tissues and cancer cell lines.

Disease relevance. Birk-Landau-Perez syndrome (BILAPES) [MIM:617595] An autosomal recessive syndrome characterized by early-childhood onset of different combinations of intellectual disability, muscle weakness, camptocormia, oculomotor apraxia, and nephropathy. The disease is caused by variants affecting the gene represented in this entry.

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

RefSeq proteins (1): NP_006336* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002524	Cation_efflux	Family
IPR009061	DNA-bd_dom_put_sf	Homologous_superfamily
IPR027469	Cation_efflux_TMD_sf	Homologous_superfamily
IPR037129	XPA_sf	Homologous_superfamily
IPR040177	SLC30A9	Family
IPR058533	Cation_efflux_TM	Domain

Pfam: PF01545

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (22 total): transmembrane region 5, sequence variant 4, helix 4, sequence conflict 3, strand 3, transit peptide 1, chain 1, short sequence motif 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2ENK	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PML9-F1	75.06	0.44

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 243 (showing top): GOBP_TRANSITION_METAL_ION_TRANSPORT, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_REGULATION_OF_MITOCHONDRION_ORGANIZATION, GOBP_NUCLEOTIDE_EXCISION_REPAIR, GOBP_DNA_DAMAGE_RESPONSE, GOCC_MITOCHONDRIAL_ENVELOPE, SCHLOSSER_SERUM_RESPONSE_DN, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, MODULE_544, GOBP_MONOATOMIC_ION_HOMEOSTASIS, COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_DN, RIGGINS_TAMOXIFEN_RESISTANCE_DN, GOBP_TRANSMEMBRANE_TRANSPORT, GOMF_CHROMATIN_BINDING, GOBP_HOMEOSTATIC_PROCESS

GO Biological Process (9): nucleotide-excision repair (GO:0006289), zinc ion transport (GO:0006829), intracellular zinc ion homeostasis (GO:0006882), regulation of mitochondrion organization (GO:0010821), positive regulation of transcription by RNA polymerase II (GO:0045944), monoatomic ion transport (GO:0006811), monoatomic cation transport (GO:0006812), transmembrane transport (GO:0055085), zinc ion transmembrane transport (GO:0071577)

GO Molecular Function (6): chromatin binding (GO:0003682), transcription coactivator activity (GO:0003713), zinc ion transmembrane transporter activity (GO:0005385), antiporter activity (GO:0015297), nuclear receptor binding (GO:0016922), monoatomic cation transmembrane transporter activity (GO:0008324)

GO Cellular Component (7): nucleus (GO:0005634), mitochondrion (GO:0005739), endoplasmic reticulum (GO:0005783), cytoskeleton (GO:0005856), cytoplasmic vesicle (GO:0031410), mitochondrial membrane (GO:0031966), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	3
cytoplasm	3
positive regulation of DNA-templated transcription	2
transport	2
monoatomic cation transmembrane transport	2
DNA repair	1
transition metal ion transport	1
intracellular monoatomic cation homeostasis	1
inorganic ion homeostasis	1
mitochondrion organization	1
regulation of organelle organization	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
monoatomic ion transport	1
cellular process	1
zinc ion transport	1
binding	1
transcription coregulator activity	1
transition metal ion transmembrane transporter activity	1
zinc ion transmembrane transport	1
secondary active transmembrane transporter activity	1
RNA polymerase II-specific DNA-binding transcription factor binding	1
monoatomic ion transmembrane transporter activity	1
endomembrane system	1
intracellular membraneless organelle	1
intracellular vesicle	1
mitochondrion	1
mitochondrial envelope	1
organelle membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1866 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC30A9	SLC30A5	Q8TAD4	841
SLC30A9	SLC30A6	Q6NXT4	838
SLC30A9	SLC30A7	Q8NEW0	828
SLC30A9	SLC30A4	O14863	817
SLC30A9	SLC30A1	Q9Y6M5	810
SLC30A9	SLC30A2	Q9BRI3	808
SLC30A9	SLC39A9	Q9NUM3	796
SLC30A9	SLC39A7	Q92504	794
SLC30A9	SLC39A11	Q8N1S5	792
SLC30A9	ACADM	P11310	790
SLC30A9	SLC30A3	Q99726	777
SLC30A9	SLC30A10	Q6XR72	763
SLC30A9	SLC39A1	Q9NY26	735
SLC30A9	SLC39A6	Q13433	720
SLC30A9	SLC39A10	Q9ULF5	714

IntAct

86 interactions, top by confidence:

A	B	Type	Score
NUF2	NDC80	psi-mi:“MI:0914”(association)	0.950
VAPB	FAM83G	psi-mi:“MI:0914”(association)	0.730
	PMPCB	psi-mi:“MI:0914”(association)	0.640
GYPA	TCAF2	psi-mi:“MI:0914”(association)	0.640
COX5A	COX7A2L	psi-mi:“MI:0914”(association)	0.530
VSIG4	TCAF2	psi-mi:“MI:0914”(association)	0.530
TBC1D15	MYO9A	psi-mi:“MI:0914”(association)	0.530
CD70	METTL15	psi-mi:“MI:0914”(association)	0.530
TBC1D15	UBXN8	psi-mi:“MI:0914”(association)	0.530
TNFSF8	LGALS8	psi-mi:“MI:0914”(association)	0.530
GORASP1	PPP6R2	psi-mi:“MI:0914”(association)	0.530
PCDHGB1	FAM171A2	psi-mi:“MI:0914”(association)	0.530
PNMA2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
HTRA2	HAX1	psi-mi:“MI:2364”(proximity)	0.420
E5	ESYT2	psi-mi:“MI:0914”(association)	0.350
	ESYT2	psi-mi:“MI:0914”(association)	0.350
P2RY6	ESYT2	psi-mi:“MI:0914”(association)	0.350
UNC93B1		psi-mi:“MI:0914”(association)	0.350
P2RY6		psi-mi:“MI:0914”(association)	0.350
P2RY6	RAVER1	psi-mi:“MI:0914”(association)	0.350
ERGIC3	TMEM223	psi-mi:“MI:0914”(association)	0.350
TBC1D15	UBXN8	psi-mi:“MI:0914”(association)	0.350
VNN2	ATP2A1	psi-mi:“MI:0914”(association)	0.350
HLA-DQA1	HLA-A	psi-mi:“MI:0914”(association)	0.350
MTRES1	UQCRH	psi-mi:“MI:0914”(association)	0.350
MTRES1	MRPL33	psi-mi:“MI:0914”(association)	0.350
	PLEKHG3	psi-mi:“MI:0914”(association)	0.350

BioGRID (195): SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS), SLC30A9 (Affinity Capture-MS)

ESM2 similar proteins: A1A4L1, A4QP75, B0S6U7, E1BPN0, E7FCP8, O00142, O55171, P0C1Q3, P19686, P19687, P33402, P49753, P57075, Q02108, Q08CH3, Q1L5Z9, Q1LWG4, Q3B8B2, Q3SZV6, Q3UUI3, Q4V8A1, Q4ZHS0, Q502J0, Q566R0, Q58CX2, Q5IRJ6, Q5R4H0, Q5R8E4, Q5SY16, Q5ZIU8, Q60963, Q63159, Q66GI4, Q6GLK2, Q6PML9, Q6TEC1, Q810S1, Q8BMS4, Q8BWM0, Q8N159

Diamond homologs: Q5IRJ6, Q5PQZ3, Q5R4H0, Q64029, Q6DCE3, Q6PML9, Q8H1G3, O59753, P23025, P27088, P27089, P28518, P28519, P53709, Q64267, V6F235

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SLC30A9	“down-regulates quantity by destabilization”	NUMB	ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	3
Uncertain significance	58
Likely benign	8
Benign	9

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
3769130	NM_006345.4(SLC30A9):c.143C>A (p.Ser48Ter)	Pathogenic
431049	NM_006345.4(SLC30A9):c.1049_1051del (p.Ala350del)	Pathogenic
1333196	NM_006345.4(SLC30A9):c.840+1G>A	Likely pathogenic
1723220	NM_006345.4(SLC30A9):c.543G>A (p.Trp181Ter)	Likely pathogenic
3377089	NM_006345.4(SLC30A9):c.841-1G>A	Likely pathogenic

SpliceAI

2807 predictions. Top by Δscore:

Variant	Effect	Δscore
4:42001614:A:AG	acceptor_gain	1.0000
4:42001615:G:GG	acceptor_gain	1.0000
4:42001615:GA:G	acceptor_gain	1.0000
4:42001778:CAGGT:C	donor_loss	1.0000
4:42001779:AGGT:A	donor_loss	1.0000
4:42001781:G:C	donor_loss	1.0000
4:42001782:T:G	donor_loss	1.0000
4:42018097:A:AG	acceptor_gain	1.0000
4:42018100:A:AG	acceptor_gain	1.0000
4:42018101:A:G	acceptor_gain	1.0000
4:42018110:GCA:G	acceptor_gain	1.0000
4:42018166:AAGAG:A	donor_loss	1.0000
4:42018167:AGAGG:A	donor_loss	1.0000
4:42018168:GAGGT:G	donor_loss	1.0000
4:42018169:AGG:A	donor_loss	1.0000
4:42018170:GG:G	donor_loss	1.0000
4:42018171:GTAA:G	donor_loss	1.0000
4:42020412:TTAG:T	acceptor_gain	1.0000
4:42020413:TAGT:T	acceptor_gain	1.0000
4:42020414:A:AG	acceptor_gain	1.0000
4:42020415:G:GA	acceptor_gain	1.0000
4:42020415:GTT:G	acceptor_gain	1.0000
4:42020415:GTTA:G	acceptor_gain	1.0000
4:42020511:TCCAG:T	donor_loss	1.0000
4:42020512:CCAG:C	donor_loss	1.0000
4:42020513:CAG:C	donor_loss	1.0000
4:42020514:AGG:A	donor_loss	1.0000
4:42020515:GG:G	donor_loss	1.0000
4:42020517:T:A	donor_loss	1.0000
4:42022836:A:AG	acceptor_gain	1.0000

AlphaMissense

3662 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:42075712:G:C	A492P	1.000
4:42020506:T:C	L142P	0.999
4:42049447:G:C	A270P	0.999
4:42049467:T:A	D276E	0.999
4:42049467:T:G	D276E	0.999
4:42070688:T:A	V472E	0.999
4:42075658:G:C	A474P	0.999
4:42075707:T:C	F490S	0.999
4:42075713:C:A	A492E	0.999
4:42075730:G:A	G498R	0.999
4:42075730:G:C	G498R	0.999
4:42075730:G:T	G498W	0.999
4:42075731:G:A	G498E	0.999
4:42075740:T:A	V501D	0.999
4:42078243:T:C	L527P	0.999
4:42078266:G:A	G535R	0.999
4:42078266:G:C	G535R	0.999
4:42078267:G:A	G535E	0.999
4:42078290:G:A	G543R	0.999
4:42078290:G:C	G543R	0.999
4:42078291:G:A	G543E	0.999
4:42078309:T:C	L549P	0.999
4:42078313:G:C	E550D	0.999
4:42078313:G:T	E550D	0.999
4:42078321:T:C	L553P	0.999
4:42086113:T:C	L565S	0.999
4:42086117:G:C	E566D	0.999
4:42086117:G:T	E566D	0.999
4:42020487:G:C	A136P	0.998
4:42020488:C:A	A136E	0.998

dbSNP variants (sampled 300 via entrez): RS1000013107 (4:42014384 A>G), RS1000030724 (4:42056758 C>T), RS1000033635 (4:41993815 G>C), RS1000074804 (4:42050969 G>T), RS1000107681 (4:42043946 A>G), RS1000115208 (4:42007132 GTAA>G), RS1000126478 (4:42045012 A>G), RS10001295 (4:42084432 T>A,C,G), RS1000133443 (4:42090921 T>C), RS1000152348 (4:42033191 T>A,C), RS1000189629 (4:42005718 C>T), RS10002107 (4:42085529 A>C,G,T), RS1000226500 (4:42032874 C>T), RS1000318585 (4:42058457 C>G), RS1000383430 (4:42078580 C>T)

Disease associations

OMIM: gene MIM:604604 | disease phenotypes: MIM:617595

GenCC curated gene-disease

Disease	Classification	Inheritance
psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Strong	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome	Definitive	AR

Mondo (1): psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome (MONDO:0044726)

Orphanet (1): Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome (Orphanet:505242)

HPO phenotypes

44 total (30 of 44 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000083	Renal insufficiency
HP:0000089	Renal hypoplasia
HP:0000252	Microcephaly
HP:0000297	Facial hypotonia
HP:0000408	Progressive sensorineural hearing impairment
HP:0000486	Strabismus
HP:0000508	Ptosis
HP:0000527	Long eyelashes
HP:0000582	Upslanted palpebral fissure
HP:0000648	Optic atrophy
HP:0000657	Oculomotor apraxia
HP:0000750	Delayed speech and language development
HP:0000822	Hypertension
HP:0001195	Single umbilical artery
HP:0001263	Global developmental delay
HP:0001266	Choreoathetosis
HP:0001274	Agenesis of corpus callosum
HP:0001288	Gait disturbance
HP:0001302	Pachygyria
HP:0001332	Dystonia
HP:0001510	Growth delay
HP:0001511	Intrauterine growth retardation
HP:0001531	Failure to thrive in infancy
HP:0001970	Tubulointerstitial nephritis
HP:0002070	Limb ataxia
HP:0002153	Hyperkalemia
HP:0002376	Developmental regression
HP:0002509	Limb hypertonia
HP:0002643	Neonatal respiratory distress

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST005355_3	Helping behaviour (self reported)	5.000000e-07
GCST005355_5	Helping behaviour (self reported)	3.000000e-06
GCST005839_40	Depression	3.000000e-09
GCST009600_120	Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)	3.000000e-10
GCST009852_1	Opioid exposure	7.000000e-08
GCST012490_511	Femur bone mineral density x serum urate levels interaction	4.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009937	Opioid use measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs1047626	Toxicity	3	aspirin	Aspirin-induced asthma

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs1047626	SLC30A9	3	3.00	1	aspirin

GtoPdb / IUPHAR curated pharmacology

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

Target class: transporter — SLC30 zinc transporter family

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, affects binding, affects folding, decreases reaction, affects cotreatment (+1 more)	3
bisphenol AF	increases reaction, increases expression, affects binding, affects folding, decreases reaction	3
bisphenol S	affects binding, affects folding, decreases reaction, increases expression	2
Estradiol	affects binding, increases reaction	2
Valproic Acid	affects expression, increases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
arsenite	affects binding, decreases reaction	1
methylparaben	decreases expression	1
sodium arsenite	decreases expression	1
Grape Seed Proanthocyanidins	decreases expression	1
jinfukang	decreases expression	1
(+)-JQ1 compound	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Environmental Pollutants	affects expression	1
Plant Extracts	affects cotreatment, increases expression	1
Thiram	decreases expression	1
Zinc	increases transport	1
Zidovudine	increases expression	1
Metribolone	affects binding, affects folding, increases reaction	1
Cyclosporine	decreases expression	1
Sodium Selenite	increases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	increases abundance, decreases expression	1

Cellosaurus cell lines

2 cell lines: 1 transformed cell line, 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D9RY	Ubigene HEK293 SLC30A9 KO	Transformed cell line	Female
CVCL_TM96	HAP1 SLC30A9 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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