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.	91252
Gene name Gene Name - the full gene name approved by the HGNC.	Solute carrier family 39 member 13
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SLC39A13
Synonyms (NCBI Gene) Gene synonyms aliases	EDSSPD3, LZT-Hs9, SCDEDS, ZIP13
Disease Acronyms (UniProt) Disease acronyms from UniProt database	EDSSPD3
Chromosome Chromosome number	11
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	11p11.2
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a member of the LIV-1 subfamily of the ZIP transporter family. The encoded transmembrane protein functions as a zinc transporter. Mutations in this gene have been associated with the spondylocheiro dysplastic form of Ehlers-Danlos syndro

Show/Hide all(5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121434363	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs140574574	C>A,T	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant
rs140597965	T>C	Likely-benign, conflicting-interpretations-of-pathogenicity	Intron variant
rs148291843	C>G	Benign, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, missense variant, coding sequence variant
rs753665968	T>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, non coding transcript variant

Show/Hide all(81)

miRTarBase ID	miRNA	Experiments	Reference
MIRT042304	hsa-miR-484	CLASH	23622248
MIRT720683	hsa-miR-3943	HITS-CLIP	19536157
MIRT720681	hsa-miR-4286	HITS-CLIP	19536157
MIRT720682	hsa-miR-6801-3p	HITS-CLIP	19536157
MIRT720680	hsa-miR-6810-3p	HITS-CLIP	19536157
MIRT720679	hsa-miR-6752-3p	HITS-CLIP	19536157
MIRT720678	hsa-miR-6734-3p	HITS-CLIP	19536157
MIRT720677	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT720676	hsa-miR-1225-3p	HITS-CLIP	19536157
MIRT720675	hsa-miR-1233-3p	HITS-CLIP	19536157
MIRT720674	hsa-miR-4313	HITS-CLIP	19536157
MIRT720673	hsa-miR-938	HITS-CLIP	19536157
MIRT720672	hsa-miR-6886-3p	HITS-CLIP	19536157
MIRT720671	hsa-miR-2355-5p	HITS-CLIP	19536157
MIRT720683	hsa-miR-3943	HITS-CLIP	19536157
MIRT720681	hsa-miR-4286	HITS-CLIP	19536157
MIRT720682	hsa-miR-6801-3p	HITS-CLIP	19536157
MIRT720680	hsa-miR-6810-3p	HITS-CLIP	19536157
MIRT720679	hsa-miR-6752-3p	HITS-CLIP	19536157
MIRT720678	hsa-miR-6734-3p	HITS-CLIP	19536157
MIRT720677	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT720676	hsa-miR-1225-3p	HITS-CLIP	19536157
MIRT720675	hsa-miR-1233-3p	HITS-CLIP	19536157
MIRT720674	hsa-miR-4313	HITS-CLIP	19536157
MIRT720673	hsa-miR-938	HITS-CLIP	19536157
MIRT720672	hsa-miR-6886-3p	HITS-CLIP	19536157
MIRT720671	hsa-miR-2355-5p	HITS-CLIP	19536157
MIRT1363325	hsa-miR-125a-5p	CLIP-seq
MIRT1363326	hsa-miR-125b	CLIP-seq
MIRT1363327	hsa-miR-1915	CLIP-seq
MIRT1363328	hsa-miR-3151	CLIP-seq
MIRT1363329	hsa-miR-3663-3p	CLIP-seq
MIRT1363330	hsa-miR-3915	CLIP-seq
MIRT1363331	hsa-miR-3928	CLIP-seq
MIRT1363332	hsa-miR-4283	CLIP-seq
MIRT1363333	hsa-miR-4319	CLIP-seq
MIRT1363334	hsa-miR-4436b-3p	CLIP-seq
MIRT1363335	hsa-miR-4481	CLIP-seq
MIRT1363336	hsa-miR-4489	CLIP-seq
MIRT1363337	hsa-miR-4492	CLIP-seq
MIRT1363338	hsa-miR-4498	CLIP-seq
MIRT1363339	hsa-miR-4505	CLIP-seq
MIRT1363340	hsa-miR-4663	CLIP-seq
MIRT1363341	hsa-miR-4685-5p	CLIP-seq
MIRT1363342	hsa-miR-4700-3p	CLIP-seq
MIRT1363343	hsa-miR-4726-3p	CLIP-seq
MIRT1363344	hsa-miR-4731-5p	CLIP-seq
MIRT1363345	hsa-miR-4745-5p	CLIP-seq
MIRT1363346	hsa-miR-4758-5p	CLIP-seq
MIRT1363347	hsa-miR-4795-5p	CLIP-seq
MIRT1363348	hsa-miR-491-5p	CLIP-seq
MIRT1363349	hsa-miR-512-3p	CLIP-seq
MIRT1363350	hsa-miR-544b	CLIP-seq
MIRT1363351	hsa-miR-762	CLIP-seq
MIRT1363352	hsa-miR-9	CLIP-seq
MIRT1363353	hsa-miR-1200	CLIP-seq
MIRT1363354	hsa-miR-1203	CLIP-seq
MIRT1363355	hsa-miR-339-3p	CLIP-seq
MIRT1363356	hsa-miR-4324	CLIP-seq
MIRT1363350	hsa-miR-544b	CLIP-seq
MIRT1363357	hsa-miR-549	CLIP-seq
MIRT1363344	hsa-miR-4731-5p	CLIP-seq
MIRT2107762	hsa-miR-1295	CLIP-seq
MIRT1363339	hsa-miR-4505	CLIP-seq
MIRT2107763	hsa-miR-4640-5p	CLIP-seq
MIRT2107764	hsa-miR-4726-5p	CLIP-seq
MIRT1363344	hsa-miR-4731-5p	CLIP-seq
MIRT1363350	hsa-miR-544b	CLIP-seq
MIRT1363344	hsa-miR-4731-5p	CLIP-seq
MIRT1363350	hsa-miR-544b	CLIP-seq
MIRT2440532	hsa-miR-1207-5p	CLIP-seq
MIRT2440533	hsa-miR-4284	CLIP-seq
MIRT2440534	hsa-miR-4437	CLIP-seq
MIRT2440535	hsa-miR-4446-3p	CLIP-seq
MIRT1363344	hsa-miR-4731-5p	CLIP-seq
MIRT2440536	hsa-miR-4763-3p	CLIP-seq
MIRT2440532	hsa-miR-1207-5p	CLIP-seq
MIRT2440533	hsa-miR-4284	CLIP-seq
MIRT2440534	hsa-miR-4437	CLIP-seq
MIRT2440535	hsa-miR-4446-3p	CLIP-seq
MIRT2440536	hsa-miR-4763-3p	CLIP-seq

Show/Hide all(19)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005385	Function	Zinc ion transmembrane transporter activity	IBA	21873635
GO:0005385	Function	Zinc ion transmembrane transporter activity	IC	18985159
GO:0005385	Function	Zinc ion transmembrane transporter activity	IDA	21917916
GO:0005515	Function	Protein binding	IPI	25416956, 32296183
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005794	Component	Golgi apparatus	IDA	21917916
GO:0005794	Component	Golgi apparatus	ISS	18985159
GO:0006882	Process	Cellular zinc ion homeostasis	IBA	21873635
GO:0006882	Process	Cellular zinc ion homeostasis	IDA	21917916
GO:0006882	Process	Cellular zinc ion homeostasis	ISS	18985159
GO:0010043	Process	Response to zinc ion	IEA
GO:0016021	Component	Integral component of membrane	IDA	21917916
GO:0030173	Component	Integral component of Golgi membrane	IC	21917916
GO:0042803	Function	Protein homodimerization activity	IPI	21917916
GO:0048471	Component	Perinuclear region of cytoplasm	ISS	18985159
GO:0061448	Process	Connective tissue development	IMP	18985159
GO:0071577	Process	Zinc ion transmembrane transport	IBA	21873635
GO:0071577	Process	Zinc ion transmembrane transport	IDA	21917916
GO:0071577	Process	Zinc ion transmembrane transport	ISS	18985159

MIM	HGNC	e!Ensembl
608735	20859	ENSG00000165915

Protein

UniProt ID

Q96H72

Protein name

Zinc transporter ZIP13 (LIV-1 subfamily of ZIP zinc transporter 9) (LZT-Hs9) (Solute carrier family 39 member 13) (Zrt- and Irt-like protein 13) (ZIP-13)

Protein function

Functions as a zinc transporter transporting Zn(2+) from the Golgi apparatus to the cytosol and thus influences the zinc level at least in areas of the cytosol (PubMed:21917916, PubMed:23213233). May regulate beige adipocyte differentiation (By

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02535	Zip	65 → 205	ZIP Zinc transporter	Family
PF02535	Zip	171 → 367	ZIP Zinc transporter	Family

Sequence

MPGCPCPGCGMAGPRLLFLTALALELLERAGGSQPALRSRGTATACRLDNKESESWGALL
SGERLDTWICSLLGSLMVGLSGVFPLLVIPLEMGTMLRSEAGAWRLKQLLSFALGGLLGN
VFLHLLPEAWAYTCSASPGGEGQSLQQQQQLGLWVIAGILTFLALEKMFLDSKEEGTSQA
PNKDPTAAAAALNGGHCLAQPAAEPGLGAVVRSIKVSGYLNLLANTIDNFTHGLAVAASF
LVSKKIGLLTTMAILLHEIPHEVGDFAILLRAGFDRWSAAKLQLSTALGGLLGAGFAICT
QSPKGVVGCSPAAEETAAWVLPFTSGGFLYIALVNVLPDLLEEEDPWRSLQQLLLLCAGI
VVMVLFSLFVD

Sequence length

371

Interactions

View interactions

	KEGG
	Alzheimer disease Parkinson disease

Show/Hide Causal Diseases (4)

Disease term	Disease name	dbSNP ID	References
Causal
Connective tissue disease	Connective Tissue Diseases	rs5742905, rs80338688, rs80356506, rs104894800, rs104894948, rs28931614, rs121913482, rs28933068, rs121913483, rs137854464, rs121912870, rs387906980, rs587777352, rs527236145, rs189754995 View all (12 more)	18985159, 22228435
Ehlers-danlos syndrome	Ehlers-Danlos Syndrome, Ehlers-Danlos Syndrome, Type IV	rs121917817, rs121917818, rs28937869, rs764070148, rs144556766, rs121913550, rs121913552, rs80338764, rs121912933, rs786205103, rs786205104, rs121912930, rs397509369, rs113485686, rs121912914 View all (490 more)	18985159
Osteochondrodysplasia	Osteochondrodysplasias	rs386833498, rs104893919, rs104893916, rs386833492, rs121908078, rs386833497, rs386833507, rs200963884, rs121908077, rs786204675, rs763198695, rs1554095433, rs766836061
Skeletal dysplasia	Skeletal dysplasia	rs121912632, rs121912633, rs121912634, rs121912636, rs121912637, rs267607147, rs387906324, rs267607150, rs397514473, rs398123438, rs515726153, rs515726154, rs515726162, rs515726163, rs515726172, rs757011098 View all (1 more)

Show/Hide Unknown Diseases (7)

Disease term	Disease name	Evidence	Source
Unknown
Spondyloenchondrodysplasia With Abnormal Dentition	spondyloepimetaphyseal dysplasia-abnormal dentition syndrome		GenCC
Ehlers-Danlos Syndrome	Ehlers-Danlos syndrome, spondylocheirodysplastic type		GenCC
Neuroticism	Neuroticism		GWAS
Kidney Disease	Kidney Disease		GWAS
Prostate cancer	Prostate cancer	Together, these results show that PRRX2 is an oncogene and might play a role in the aggressiveness of PC within the DNPC population.	GWAS, CBGDA
Hypertension	Hypertension		GWAS
Insomnia	Insomnia		GWAS

Show/Hide Text Mining Associations (15)

Disease Name	Relationship Type	References
Associations from Text Mining
Body Dysmorphic Disorders	Associate	32295219
Breast Neoplasms	Associate	32744318
Cognition Disorders	Associate	27211562
Connective Tissue Diseases	Associate	32295219
Developmental Disabilities	Associate	27211562
Dysplastic Nevus Syndrome	Associate	18513683, 23213233
Ehlers Danlos Syndrome	Associate	18513683, 23213233, 32295219
Ehlers Danlos syndrome type 3	Associate	18513683, 28882145, 32295219
Growth Disorders	Associate	32295219
Keratoconus	Associate	32295219
Psychotic Disorders	Associate	27211562
Schizophrenia	Associate	27211562
Spinal Diseases	Associate	32295219
Spondylocheirodysplasia Ehlers Danlos Syndrome Like	Associate	23213233, 32295219
Stroke	Associate	32295219

SLC39A13 (solute carrier family 39 member 13)