SLC30A1
Basic information
Region (hg38): 1:211571568-211579161
Previous symbols: [ "ZNT1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (30 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC30A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021194.3. 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 | 30 | 30 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 30 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC30A1 | protein_coding | protein_coding | ENST00000367001 | 2 | 7175 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.985 | 0.0147 | 122679 | 0 | 1 | 122680 | 0.00000408 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.20 | 183 | 288 | 0.635 | 0.0000132 | 3306 |
| Missense in Polyphen | 31 | 106.05 | 0.29231 | 1204 | ||
| Synonymous | 0.653 | 105 | 114 | 0.922 | 0.00000553 | 1056 |
| Loss of Function | 3.32 | 0 | 12.8 | 0.00 | 6.09e-7 | 159 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000291 | 0.0000291 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in zinc transport out of the cell.;
- Pathway
- Mineral absorption - Homo sapiens (human);Zinc homeostasis;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 efflux and compartmentalization by the SLC30 family;Zinc transporters
(Consensus)
Recessive Scores
- pRec
- 0.210
Intolerance Scores
- loftool
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.42
Haploinsufficiency Scores
- pHI
- 0.458
- hipred
- Y
- hipred_score
- 0.664
- ghis
- 0.566
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.123
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc30a1
- Phenotype
- reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype;
Gene ontology
- Biological process
- in utero embryonic development;zinc ion transport;cellular calcium ion homeostasis;cellular zinc ion homeostasis;negative regulation of neurotransmitter secretion;calcium ion import;cadmium ion transmembrane transport;zinc ion transmembrane transport;negative regulation of zinc ion transmembrane import;detoxification of cadmium ion;negative regulation of calcium ion import
- Cellular component
- cytoplasm;endoplasmic reticulum;Golgi apparatus;plasma membrane;T-tubule;nuclear membrane;Schaffer collateral - CA1 synapse;integral component of postsynaptic density membrane
- Molecular function
- zinc ion transmembrane transporter activity;protein binding;calcium channel inhibitor activity