Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	55532
Gene name Gene Name - the full gene name approved by the HGNC.	Solute carrier family 30 member 10
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SLC30A10
Synonyms (NCBI Gene) Gene synonyms aliases	HMDPC, HMNDYT1, ZNT10, ZNT8, ZRC1, ZnT-10
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1q41
Summary Summary of gene provided in NCBI Entrez Gene.	This gene is highly expressed in the liver and is inducible by manganese. Its protein product appears to be critical in maintaining manganese levels, and has higher specificity for manganese than zinc. Loss of function mutations appear to result in a pleo

Show/Hide all(5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs281860289	CAC>-	Pathogenic	Non coding transcript variant, inframe deletion, coding sequence variant
rs281860290	G>A	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs281860291	A>G	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs281860292	T>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs770740586	G>A	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant

Show/Hide all(110)

miRTarBase ID	miRNA	Experiments	Reference
MIRT030334	hsa-miR-26b-5p	Microarray	19088304
MIRT717620	hsa-miR-3189-3p	HITS-CLIP	19536157
MIRT717619	hsa-miR-635	HITS-CLIP	19536157
MIRT717618	hsa-miR-6774-5p	HITS-CLIP	19536157
MIRT717617	hsa-miR-4424	HITS-CLIP	19536157
MIRT717616	hsa-miR-3945	HITS-CLIP	19536157
MIRT717615	hsa-miR-4253	HITS-CLIP	19536157
MIRT717614	hsa-miR-6862-5p	HITS-CLIP	19536157
MIRT717613	hsa-miR-335-3p	HITS-CLIP	19536157
MIRT639442	hsa-miR-455-3p	HITS-CLIP	23824327
MIRT639441	hsa-miR-6516-5p	HITS-CLIP	23824327
MIRT639440	hsa-miR-450b-5p	HITS-CLIP	23824327
MIRT639439	hsa-miR-507	HITS-CLIP	23824327
MIRT639438	hsa-miR-557	HITS-CLIP	23824327
MIRT639437	hsa-miR-3680-3p	HITS-CLIP	23824327
MIRT639436	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT446086	hsa-miR-4724-5p	PAR-CLIP	22100165
MIRT446087	hsa-miR-5584-3p	PAR-CLIP	22100165
MIRT446085	hsa-miR-4539	PAR-CLIP	22100165
MIRT446084	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT446083	hsa-miR-1303	PAR-CLIP	22100165
MIRT446086	hsa-miR-4724-5p	PAR-CLIP	22100165
MIRT446087	hsa-miR-5584-3p	PAR-CLIP	22100165
MIRT446085	hsa-miR-4539	PAR-CLIP	22100165
MIRT446084	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT446083	hsa-miR-1303	PAR-CLIP	22100165
MIRT639442	hsa-miR-455-3p	PAR-CLIP	27292025
MIRT639441	hsa-miR-6516-5p	PAR-CLIP	27292025
MIRT717620	hsa-miR-3189-3p	HITS-CLIP	19536157
MIRT717619	hsa-miR-635	HITS-CLIP	19536157
MIRT717618	hsa-miR-6774-5p	HITS-CLIP	19536157
MIRT717617	hsa-miR-4424	HITS-CLIP	19536157
MIRT717616	hsa-miR-3945	HITS-CLIP	19536157
MIRT717615	hsa-miR-4253	HITS-CLIP	19536157
MIRT717614	hsa-miR-6862-5p	HITS-CLIP	19536157
MIRT717613	hsa-miR-335-3p	HITS-CLIP	19536157
MIRT639442	hsa-miR-455-3p	HITS-CLIP	23824327
MIRT639441	hsa-miR-6516-5p	HITS-CLIP	23824327
MIRT639440	hsa-miR-450b-5p	HITS-CLIP	23824327
MIRT639439	hsa-miR-507	HITS-CLIP	23824327
MIRT639438	hsa-miR-557	HITS-CLIP	23824327
MIRT639437	hsa-miR-3680-3p	HITS-CLIP	23824327
MIRT639436	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT446086	hsa-miR-4724-5p	PAR-CLIP	22100165
MIRT446087	hsa-miR-5584-3p	PAR-CLIP	22100165
MIRT446085	hsa-miR-4539	PAR-CLIP	22100165
MIRT446084	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT446083	hsa-miR-1303	PAR-CLIP	22100165
MIRT446086	hsa-miR-4724-5p	PAR-CLIP	22100165
MIRT446087	hsa-miR-5584-3p	PAR-CLIP	22100165
MIRT446085	hsa-miR-4539	PAR-CLIP	22100165
MIRT446084	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT446083	hsa-miR-1303	PAR-CLIP	22100165
MIRT1359057	hsa-miR-103a	CLIP-seq
MIRT1359058	hsa-miR-107	CLIP-seq
MIRT1359059	hsa-miR-1276	CLIP-seq
MIRT1359060	hsa-miR-132	CLIP-seq
MIRT1359061	hsa-miR-148a	CLIP-seq
MIRT1359062	hsa-miR-148b	CLIP-seq
MIRT1359063	hsa-miR-152	CLIP-seq
MIRT1359064	hsa-miR-15a	CLIP-seq
MIRT1359065	hsa-miR-15b	CLIP-seq
MIRT1359066	hsa-miR-16	CLIP-seq
MIRT1359067	hsa-miR-195	CLIP-seq
MIRT1359068	hsa-miR-21	CLIP-seq
MIRT1359069	hsa-miR-212	CLIP-seq
MIRT1359070	hsa-miR-2278	CLIP-seq
MIRT1359071	hsa-miR-2682	CLIP-seq
MIRT1359072	hsa-miR-3145-3p	CLIP-seq
MIRT1359073	hsa-miR-3714	CLIP-seq
MIRT1359074	hsa-miR-424	CLIP-seq
MIRT1359075	hsa-miR-4276	CLIP-seq
MIRT1359076	hsa-miR-4311	CLIP-seq
MIRT1359077	hsa-miR-449c	CLIP-seq
MIRT1359078	hsa-miR-4659a-3p	CLIP-seq
MIRT1359079	hsa-miR-4659b-3p	CLIP-seq
MIRT1359080	hsa-miR-494	CLIP-seq
MIRT1359081	hsa-miR-497	CLIP-seq
MIRT1359082	hsa-miR-583	CLIP-seq
MIRT1359083	hsa-miR-590-5p	CLIP-seq
MIRT1922379	hsa-miR-3613-3p	CLIP-seq
MIRT1922380	hsa-miR-3646	CLIP-seq
MIRT1922381	hsa-miR-3662	CLIP-seq
MIRT1922382	hsa-miR-4272	CLIP-seq
MIRT2330608	hsa-miR-1229	CLIP-seq
MIRT2330609	hsa-miR-27a	CLIP-seq
MIRT2330610	hsa-miR-27b	CLIP-seq
MIRT2330611	hsa-miR-30a	CLIP-seq
MIRT2330612	hsa-miR-30b	CLIP-seq
MIRT2330613	hsa-miR-30c	CLIP-seq
MIRT2330614	hsa-miR-30d	CLIP-seq
MIRT2330615	hsa-miR-30e	CLIP-seq
MIRT2330616	hsa-miR-4277	CLIP-seq
MIRT2330617	hsa-miR-513a-5p	CLIP-seq
MIRT2330618	hsa-miR-548a-5p	CLIP-seq
MIRT2330619	hsa-miR-548ab	CLIP-seq
MIRT2330620	hsa-miR-548ak	CLIP-seq
MIRT2330621	hsa-miR-548b-5p	CLIP-seq
MIRT2330622	hsa-miR-548c-5p	CLIP-seq
MIRT2330623	hsa-miR-548d-5p	CLIP-seq
MIRT2330624	hsa-miR-548h	CLIP-seq
MIRT2330625	hsa-miR-548i	CLIP-seq
MIRT2330626	hsa-miR-548j	CLIP-seq
MIRT2330627	hsa-miR-548w	CLIP-seq
MIRT2330628	hsa-miR-548y	CLIP-seq
MIRT2330629	hsa-miR-559	CLIP-seq
MIRT2330630	hsa-miR-922	CLIP-seq
MIRT2624682	hsa-miR-4496	CLIP-seq
MIRT2624683	hsa-miR-4738-3p	CLIP-seq
MIRT2624684	hsa-miR-873	CLIP-seq

Show/Hide all(49)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0005384	Function	Manganese ion transmembrane transporter activity	IDA	25319704
GO:0005384	Function	Manganese ion transmembrane transporter activity	IMP	27226609, 27307044
GO:0005384	Function	Manganese ion transmembrane transporter activity	TAS
GO:0005385	Function	Zinc ion transmembrane transporter activity	IBA
GO:0005385	Function	Zinc ion transmembrane transporter activity	IDA	30755481
GO:0005385	Function	Zinc ion transmembrane transporter activity	IDA	22427991, 26728129
GO:0005515	Function	Protein binding	IPI	26728129
GO:0005768	Component	Endosome	IEA
GO:0005769	Component	Early endosome	IDA	26728129
GO:0005794	Component	Golgi apparatus	IDA	22706290, 27226609
GO:0005794	Component	Golgi apparatus	IEA
GO:0005886	Component	Plasma membrane	IDA	25319704, 27226609, 27307044
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006812	Process	Monoatomic cation transport	IEA
GO:0006828	Process	Manganese ion transport	IBA
GO:0006828	Process	Manganese ion transport	IMP	22341972, 26728129
GO:0006829	Process	Zinc ion transport	IEA
GO:0006878	Process	Intracellular copper ion homeostasis	IDA	25319704
GO:0006882	Process	Intracellular zinc ion homeostasis	IBA
GO:0006882	Process	Intracellular zinc ion homeostasis	IDA	25319704
GO:0006882	Process	Intracellular zinc ion homeostasis	IDA	22427991, 26728129
GO:0006882	Process	Intracellular zinc ion homeostasis	IMP	27226609
GO:0007173	Process	Epidermal growth factor receptor signaling pathway	IDA	26728129
GO:0008021	Component	Synaptic vesicle	IDA	26728129
GO:0008324	Function	Monoatomic cation transmembrane transporter activity	IEA
GO:0010312	Process	Detoxification of zinc ion	IBA
GO:0015297	Function	Antiporter activity	IEA
GO:0016020	Component	Membrane	IBA
GO:0016020	Component	Membrane	IEA
GO:0030026	Process	Intracellular manganese ion homeostasis	IDA	25319704
GO:0030026	Process	Intracellular manganese ion homeostasis	IMP	22341972, 27226609, 27307044
GO:0031901	Component	Early endosome membrane	IDA	22427991
GO:0031901	Component	Early endosome membrane	IEA
GO:0055037	Component	Recycling endosome	IDA	26728129
GO:0055038	Component	Recycling endosome membrane	IDA	22427991
GO:0055038	Component	Recycling endosome membrane	IEA
GO:0055071	Process	Manganese ion homeostasis	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0062111	Process	Zinc ion import into organelle	IDA	22427991
GO:0070374	Process	Positive regulation of ERK1 and ERK2 cascade	IDA	26728129
GO:0071577	Process	Zinc ion transmembrane transport	IBA
GO:0071577	Process	Zinc ion transmembrane transport	IEA
GO:0140048	Process	Manganese ion export across plasma membrane	IDA	25319704
GO:0140048	Process	Manganese ion export across plasma membrane	IMP	27307044
GO:0140983	Function	Calcium:manganese antiporter activity	IDA	30755481
GO:1904385	Process	Cellular response to angiotensin	IDA	22427991

MIM	HGNC	e!Ensembl
611146	25355	ENSG00000196660

Protein

UniProt ID

Q6XR72

Protein name

Calcium/manganese antiporter SLC30A10 (Solute carrier family 30 member 10) (Zinc transporter 10) (ZnT-10)

Protein function

Calcium:manganese antiporter of the plasma membrane mediating the efflux of intracellular manganese coupled to an active extracellular calcium exchange (PubMed:30755481). Required for intracellular manganese homeostasis, an essential cation for

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01545	Cation_efflux	11 → 307	Cation efflux family	Family

Tissue specificity

TISSUE SPECIFICITY: Specifically expressed in fetal liver and fetal brain (PubMed:15154973). Expressed in adult tissues with relative levels small intestine > liver > testes > brain > ovary > colon > cervix > prostate > placenta (PubMed:22706290). Express

Sequence

MGRYSGKTCRLLFMLVLTVAFFVAELVSGYLGNSIALLSDSFNMLSDLISLCVGLSAGYI
ARRPTRGFSATYGYARAEVVGALSNAVFLTALCFTIFVEAVLRLARPERIDDPELVLIVG
VLGLLVNVVGLLIFQDCAAWFACCLRGRSRRLQQRQQLAEGCVPGAFGGPQGAEDPRRAA
DPTAPGSDSAVTLRGTSVERKREKGATVFANVAGDSFNTQNEPEDMMKKEKKSEALNIRG
VLLHVMGDALGSVVVVITAIIFYVLPLKSEDPCNWQCYIDPSLTVLMVIIILSSAFPLIK
ETAAILLQMVPKGVNMEELMSKLSAVPGISSVHEVHIWELVSGKIIATLHIKYPKDRGYQ
DASTKIREIFHHAGIHNVTIQFENVDLKEPLEQKDLLLLCNSPCISKGCAKQLCCPPGAL
PLAHVNGCAEHNGGPSLDTYGSDGLSRRDAREVAIEVSLDSCLSDHGQSLNKTQEDQCYV
NRTHF

Sequence length

485

Interactions

View interactions

	Reactome
			Metal ion SLC transporters

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Hypermanganesemia with Dystonia Polycythemia and Cirrhosis	Hypermanganesemia with dystonia, polycythemia, and cirrhosis	rs281860285, rs281860284, rs281860288, rs281860287, rs281860292	N/A

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Cholangiocarcinoma	Extrahepatic cholangiocarcinoma	N/A	N/A	GWAS
Polycythemia	cirrhosis - dystonia - polycythemia - hypermanganesemia syndrome	N/A	N/A	GenCC
Urolithiasis	Urolithiasis	N/A	N/A	GWAS

Show/Hide Text Mining Associations (31)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Abdominal Injuries	Associate	31167208
Adenocarcinoma	Associate	35049094
Alcoholic Intoxication	Associate	27107558
Anemia Iron Deficiency	Associate	34315874
Attention Deficit Disorder with Hyperactivity	Associate	31233999
Bile Duct Neoplasms	Associate	34315874
Carcinoma Hepatocellular	Associate	32247823
Carcinoma Non Small Cell Lung	Associate	38384053
Colorectal Neoplasms	Associate	32071364, 32351322, 39596116
Colorectal Neoplasms	Inhibit	32633358
Diabetes Mellitus Type 2	Associate	31167208
Disease	Associate	22341971
Dystonia	Associate	22341971, 22341972, 22926781
Fibrosis	Associate	34315874
Glioma	Inhibit	23595627
Hematologic Neoplasms	Associate	22341971
Huntington Disease	Associate	33049985
Liver Cirrhosis	Associate	22341972, 22926781
Liver Diseases	Associate	22341971
Manganese Poisoning	Associate	30272946
Metabolic Syndrome	Associate	32247823
Neoplasm Metastasis	Inhibit	32633358
Neoplasm Metastasis	Associate	38384053
Neoplasms	Associate	32633358, 39596116
Neoplasms Adipose Tissue	Associate	32247823
Obesity	Associate	31167208
Parkinson Disease	Associate	23357421, 27107558
Parkinson Disease Secondary	Associate	22341971, 23357421, 27107558, 27307044, 30272946
Parkinsonian Disorders	Associate	30272946
Polycythemia	Associate	22341971, 22341972, 22926781
Prostatic Neoplasms	Associate	27833104, 35049094

SLC30A10 (solute carrier family 30 member 10)