SLC39A1
Basic information
Region (hg38): 1:153959099-153968184
Previous symbols: [ "ZIRTL" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (37 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001271958.2. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 36 | 37 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 36 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC39A1 | protein_coding | protein_coding | ENST00000368623 | 3 | 8614 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.126 | 0.853 | 125724 | 0 | 24 | 125748 | 0.0000954 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.953 | 145 | 181 | 0.801 | 0.00000966 | 2002 |
| Missense in Polyphen | 30 | 46.132 | 0.65031 | 581 | ||
| Synonymous | 1.21 | 73 | 87.4 | 0.835 | 0.00000464 | 791 |
| Loss of Function | 1.99 | 3 | 9.66 | 0.310 | 4.95e-7 | 107 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000294 | 0.000293 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000132 | 0.000132 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Mediates zinc uptake. May function as a major endogenous zinc uptake transporter in many cells of the body. Responsible for the rapid uptake and accumulation of physiologically effective zinc in prostate cells. {ECO:0000269|PubMed:12888280}.;
- Pathway
- Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis;Senescence and Autophagy in Cancer;Zinc influx into cells by the SLC39 gene family;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Metal ion SLC transporters;Zinc transporters
(Consensus)
Recessive Scores
- pRec
- 0.231
Intolerance Scores
- loftool
- 0.579
- rvis_EVS
- -0.6
- rvis_percentile_EVS
- 17.75
Haploinsufficiency Scores
- pHI
- 0.491
- hipred
- N
- hipred_score
- 0.242
- ghis
- 0.579
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.536
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc39a1
- Phenotype
- limbs/digits/tail phenotype; embryo phenotype; normal phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Gene ontology
- Biological process
- in utero embryonic development;cation transport;embryonic cranial skeleton morphogenesis;limb development;zinc ion transmembrane transport
- Cellular component
- endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane
- Molecular function
- signaling receptor binding;zinc ion transmembrane transporter activity;inorganic cation transmembrane transporter activity