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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	91252
Gene name	Solute carrier family 39 member 13
Gene symbol	SLC39A13
Synonyms (NCBI Gene)	EDSSPD3LZT-Hs9SCDEDSZIP13
Chromosome	11
Chromosome location	11p11.2
Summary	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 (40)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IC	21917916
GO:0000139	Component	Golgi membrane	IDA	31412620
GO:0000139	Component	Golgi membrane	IEA
GO:0005385	Function	Zinc ion transmembrane transporter activity	IBA
GO:0005385	Function	Zinc ion transmembrane transporter activity	IC	18985159
GO:0005385	Function	Zinc ion transmembrane transporter activity	IDA	21917916
GO:0005385	Function	Zinc ion transmembrane transporter activity	IMP	23213233
GO:0005515	Function	Protein binding	IPI	25416956, 32296183
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	31412620
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005794	Component	Golgi apparatus	IDA	21917916
GO:0005794	Component	Golgi apparatus	IEA
GO:0005794	Component	Golgi apparatus	ISS	18985159
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006829	Process	Zinc ion transport	IEA
GO:0006829	Process	Zinc ion transport	IMP	23213233
GO:0006882	Process	Intracellular zinc ion homeostasis	IBA
GO:0006882	Process	Intracellular zinc ion homeostasis	IDA	21917916
GO:0006882	Process	Intracellular zinc ion homeostasis	IEA
GO:0006882	Process	Intracellular zinc ion homeostasis	ISS	18985159
GO:0016020	Component	Membrane	IDA	21917916
GO:0016020	Component	Membrane	IEA
GO:0030001	Process	Metal ion transport	IEA
GO:0030659	Component	Cytoplasmic vesicle membrane	IEA
GO:0030659	Component	Cytoplasmic vesicle membrane	IMP	23213233
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0042803	Function	Protein homodimerization activity	IPI	21917916
GO:0046873	Function	Metal ion transmembrane transporter activity	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	ISS	18985159
GO:0050873	Process	Brown fat cell differentiation	IEA
GO:0050873	Process	Brown fat cell differentiation	ISS
GO:0055085	Process	Transmembrane transport	IEA
GO:0061448	Process	Connective tissue development	IEA
GO:0061448	Process	Connective tissue development	IMP	18985159
GO:0071577	Process	Zinc ion transmembrane transport	IBA
GO:0071577	Process	Zinc ion transmembrane transport	IDA	21917916
GO:0071577	Process	Zinc ion transmembrane transport	IEA
GO:0071577	Process	Zinc ion transmembrane transport	ISS	18985159

MIM	HGNC	e!Ensembl
608735	20859	ENSG00000165915

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

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Ehlers-Danlos syndrome, spondylocheirodysplastic type	Pathogenic	rs1333436792	RCV000002214	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (21)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
BONE DISEASES	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONNECTIVE TISSUE DISEASES	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Connective tissue disorder	Conflicting classifications of pathogenicity; Benign; Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CUTIS LAXA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ehlers-Danlos syndrome	Uncertain significance; Conflicting classifications of pathogenicity; Benign; Likely benign	ClinVar CTD, Disgenet CTD, Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
EHLERS-DANLOS SYNDROME, SPONDYLODYSPLASTIC TYPE, 3	—	HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fine-Lubinsky syndrome	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MITRAL VALVE PROLAPSE SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOPIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCLERODERMA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SLC39A13-related disorder	Likely benign; Conflicting classifications of pathogenicity; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPONDYLOEPIMETAPHYSEAL DYSPLASIA WITH ABNORMAL DENTITION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPONDYLOEPIMETAPHYSEAL DYSPLASIA-ABNORMAL DENTITION SYNDROME	—	GenCC	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STROKE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOOTH ABNORMALITIES	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (37)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Attention Deficit Disorder	Attention Deficit Hyperactivity Disorder	BEFREE	27211562		★★★★★ ★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	BEFREE	27211562		★★★★★ ★☆☆☆☆ Found in Text Mining only
Bone Diseases	Bone Disease	CTD_human_DG	22228435		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	32744318	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognitive disorder	BEFREE	27211562		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognition disorder	Pubtator	27211562	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Connective Tissue Diseases	Connective Tissue Disease	CTD_human_DG	18985159, 22228435		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Connective Tissue Diseases	Connective tissue disease	Pubtator	32295219	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental Disabilities	Developmental disability	Pubtator	27211562	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ehlers-Danlos Syndrome	Ehlers-Danlos Syndrome	BEFREE	18985159, 21917916, 23213233, 30610452		★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Ehlers-Danlos Syndrome	Ehlers-Danlos Syndrome	CTD_human_DG	18985159		★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Ehlers-Danlos Syndrome, Type IV	Ehlers-Danlos Syndrome	CTD_human_DG	18985159		★★★★★ ★☆☆☆☆ Found in Text Mining only
Epidermodysplasia Verruciformis	Epidermodysplasia Verruciformis	BEFREE	29439479		★★★★★ ★☆☆☆☆ Found in Text Mining only
Exophthalmos	Proptosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Fibrosarcoma	Fibrosarcoma	BEFREE	31636298		★★★★★ ★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	32295219	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypodontia	Hypodontia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	27211562		★★★★★ ★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	Pubtator	32295219	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Metabolic Syndrome X	Metabolic Syndrome	BEFREE	29415457		★★★★★ ★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	28854265, 29415457		★★★★★ ★☆☆☆☆ Found in Text Mining only
Odontome	Odontome	CTD_human_DG	18985159, 22228435		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteochondrodysplasias	Osteochondrodysplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteopenia	Osteopenia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Psychotic Disorders	Psychotic disorders	Pubtator	27211562	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	Pubtator	27211562	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Skeletal dysplasia	Skeletal Dysplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
SLC39A13-related spondylodysplastic Ehlers-Danlos syndrome	Spondylodysplastic Ehlers-Danlos Syndrome	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like	Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like	ORPHANET_DG	18513683		★★★★★ ★☆☆☆☆ Found in Text Mining only
Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like	Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like	GENOMICS_ENGLAND_DG	18985159, 28306225		★★★★★ ★☆☆☆☆ Found in Text Mining only
Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like	Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like	BEFREE	23213233		★★★★★ ★☆☆☆☆ Found in Text Mining only
Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like	Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like	Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Spondyloepimetaphyseal Dysplasia With Abnormal Dentition	Spondyloenchondrodysplasia With Abnormal Dentition	GENOMICS_ENGLAND_DG	18985159		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Stroke	Stroke	Pubtator	32295219	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

SLC39A13 (solute carrier family 39 member 13)