SLC39A5 (solute carrier family 39 member 5)

Gene

• Entrez ID: 283375
• Gene name: Solute carrier family 39 member 5
• Gene symbol: SLC39A5
• Synonyms (NCBI Gene): LZT-Hs7, MYP24, ZIP5
• Chromosome: 12
• Chromosome location: 12q13.3
• Summary: The protein encoded by this gene belongs to the ZIP family of zinc transporters that transport zinc into cells from outside, and play a crucial role in controlling intracellular zinc levels. Zinc is an essential cofactor for many enzymes and proteins invo

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs199624584	C>A,G,T	Pathogenic	Non coding transcript variant, coding sequence variant, synonymous variant, 5 prime UTR variant, stop gained
rs587777625	T>C,G	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001654	Process	Eye development	IMP	24891338
GO:0005385	Function	Zinc ion transmembrane transporter activity	IBA
GO:0005385	Function	Zinc ion transmembrane transporter activity	IEA
GO:0005385	Function	Zinc ion transmembrane transporter activity	ISS
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006829	Process	Zinc ion transport	IEA
GO:0006829	Process	Zinc ion transport	ISS
GO:0015701	Process	Bicarbonate transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016323	Component	Basolateral plasma membrane	IEA
GO:0016323	Component	Basolateral plasma membrane	ISS
GO:0030001	Process	Metal ion transport	IEA
GO:0030003	Process	Intracellular monoatomic cation homeostasis	IBA
GO:0030509	Process	BMP signaling pathway	IMP	24891338
GO:0034224	Process	Cellular response to zinc ion starvation	IEA
GO:0046873	Function	Metal ion transmembrane transporter activity	IEA
GO:0048026	Process	Positive regulation of mRNA splicing, via spliceosome	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0061351	Process	Neural precursor cell proliferation	ISS
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0070315	Process	G1 to G0 transition involved in cell differentiation	ISS
GO:0071577	Process	Zinc ion transmembrane transport	IEA
GO:0071577	Process	Zinc ion transmembrane transport	ISS
GO:0071578	Process	Zinc ion import across plasma membrane	IBA
GO:0140410	Function	Monoatomic cation:bicarbonate symporter activity	IBA

Other IDs

• MIM: 608730
• HGNC: 20502
• e!Ensembl: ENSG00000139540

Protein

• UniProt ID: Q6ZMH5
• Protein name: Zinc transporter ZIP5 (Solute carrier family 39 member 5) (Zrt- and Irt-like protein 5) (ZIP-5)
• Protein function: Uniporter that transports zinc(2+) into polarized cells of enterocytes, pancreatic acinar and endoderm cells across the basolateral membrane and participates, notably, in zinc excretion from the intestine by the uptake of zinc from the blood int
• PDB: 7Y9C, 7YF2, 7YF4
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02535	Zip	210 → 527	ZIP Zinc transporter	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed in liver, kidney, pancreas, small intestine, colon, spleen, fetal liver and fetal kidney. {ECO:0000269|PubMed:15322118}.
• Sequence:

  MMGSPVSHLLAGFCVWVVLGWVGGSVPNLGPAEQEQNHYLAQLFGLYGENGTLTAGGLAR
  LLHSLGLGRVQGLRLGQHGPLTGRAASPAADNSTHRPQNPELSVDVWAGMPLGPSGWGDL
  EESKAPHLPRGPAPSGLDLLHRLLLLDHSLADHLNEDCLNGSQLLVNFGLSPAAPLTPRQ
  FALLCPALLYQIDSRVCIGAPAPAPPGDLLSALLQSALAVLLLSLPSPLSLLLLRLLGPR
  LLRPLLGFLGALAVGTLCGDALLHLLPHAQEGRHAGPGGLPEKDLGPGLSVLGGLFLLFV
  LENMLGLLRHRGLRPRCCRRKRRNLETRNLDPENGSGMALQPLQAAPEPGAQGQREKNSQ
  HPPALAPPGHQGHSHGHQGGTDITWMVLLGDGLHNLTDGLAIGAAFSDGFSSGLSTTLAV
  FCHELPHELGDFAMLLQSGLSFRRLLLLSLVSGALGLGGAVLGVGLSLGPVPLTPWVFGV
  TAGVFLYVALVDMLPALLRPPEPLPTPHVLLQGLGLLLGGGLMLAITLLEERLLPVTTEG
  

• Sequence length: 540

Pathways

KEGG:

Alzheimer disease
Parkinson disease

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Myopia 24, autosomal dominant	Likely pathogenic; Pathogenic	rs1356255450, rs199624584, rs587777625	RCV001706763 RCV000133506 RCV000133507	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
MYOPIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SLC39A5-related disorder	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
B-Cell Lymphomas	B-Cell Lymphoma	BEFREE	27458102		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	32744318	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal carcinoma	Esophageal Carcinoma	BEFREE	26133979, 27458102		★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophagus Neoplasm	BEFREE	26133979, 27458102		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of esophagus	Esophagus Neoplasm	BEFREE	26133979, 27458102		★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	Pubtator	28442722, 34302427, 35002215, 37191617	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Myopia	Myopia	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOPIA 24, AUTOSOMAL DOMINANT	Myopia	UNIPROT_DG	24891338, 25525168		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MYOPIA 24, AUTOSOMAL DOMINANT	Myopia	CTD_human_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MYOPIA 24, AUTOSOMAL DOMINANT	Myopia	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neoplasms	Neoplasms	BEFREE	27458102		★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal detachment	Pubtator	37191617	Associate	★☆☆☆☆ Found in Text Mining only
Severe myopia	Myopia	BEFREE	24891338		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	26133979		★☆☆☆☆ Found in Text Mining only