SLC39A2
protein-codingsolute carrier family 39 member 2, the group of Solute carrier family 39
Gene summary
This gene encodes a member of the ZIP family of metal ion transporters. The encoded protein functions as a zinc transporter. Mutations in this gene may be associated with susceptibility to carotid artery disease. Multiple transcript variants have been described. [provided by RefSeq, Mar 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC39A2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014579.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 46 | 4 | 1 | 51 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 46 | 4 | 2 | 52 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055394.2 | 4 | MANE Select | |
| Ensembl | ENSP00000298681.4 | 4 | MANE Select | |
| RefSeq | NP_001243517.1 | 3 | Standard | |
| Ensembl | ENSP00000452568.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nuclear Receptors Meta-Pathway
- NRF2 pathway
- Zinc homeostasis
- Senescence and Autophagy in Cancer
- Zinc influx into cells by the SLC39 gene family
Biological Process
- zinc ion transport
- zinc ion transmembrane transport
Molecular Function
- zinc ion transmembrane transporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- cytoplasmic vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000298681
- Coding exons
- 4
- Length
- 2617
- Individuals with no LoFs
- 125390
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 354
- Defined
- 125745
- p
- 0.00141
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.467 | 185 | 168 | 1.10 | 0.00000853 | 1934 |
| Missense (PolyPhen) | 76 | 67.552 | 1.1251 | 850 | ||
| Synonymous | 0.566 | 64 | 70.0 | 0.914 | 0.00000359 | 698 |
| Loss of Function | 1.08 | 8 | 12.1 | 0.663 | 6.69e-7 | 139 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.0021 | 0.0021 | notable |
| Ashkenazi Jewish | 0.011 | 0.011 | notable |
| East Asian | 0.0016 | 0.0016 | notable |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00051 | 0.00051 | rare |
| South Asian | 0.0022 | 0.0022 | notable |
| Other | 0.0026 | 0.0026 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Mediates zinc uptake. Zinc uptake may be mediated by a Zn(2+)-HCO(3)(-) symport mechanism and can function in the presence of albumin. May also transport other divalent cations. May be important in contact inhibition of normal epithelial cells and loss of its expression may play a role in tumorigenesis.;
Recessive Scores
- pRec
- 0.0927
Intolerance Scores
- LoFtool
- 0.786
- RVIS EVS
- 1.82
- RVIS percentile EVS
- 96.97
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.124
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |