SLC30A2
Basic information
Region (hg38): 1:26037252-26046118
Previous symbols: [ "ZNT2" ]
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Zinc deficiency, transient neonata | AD | Biochemical | Infants born to mothers with causative variants can show signs of zinc deficiency, and awareness may allow zinc supplementation in the infant's diet | Biochemical | 17065149; 22733820 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (31 variants)
- Zinc_deficiency,_transient_neonatal (6 variants)
- not_provided (4 variants)
- SLC30A2-related_disorder (2 variants)
- Prostate_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC30A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001004434.3. 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 | 3 | |||||
| missense | 35 | 38 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 4 | 1 | 35 | 2 | 2 |
Highest pathogenic variant AF is 0.000022922253
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC30A2 | protein_coding | protein_coding | ENST00000374276 | 8 | 8882 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0809 | 0.917 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.928 | 185 | 224 | 0.826 | 0.0000125 | 2421 |
| Missense in Polyphen | 58 | 89.66 | 0.64689 | 1031 | ||
| Synonymous | 0.231 | 94 | 96.9 | 0.970 | 0.00000604 | 762 |
| Loss of Function | 2.71 | 5 | 17.1 | 0.292 | 8.68e-7 | 181 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000578 | 0.0000578 |
| Ashkenazi Jewish | 0.000100 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000617 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Disease
- DISEASE: Zinc deficiency, transient neonatal (TNZD) [MIM:608118]: A disorder occurring in breast-fed infants as a consequence of low milk zinc concentration in their nursing mothers, which cannot be corrected by maternal zinc supplementation. A large amount of zinc, an essential trace mineral, is required for normal growth particularly in infants, and breast milk normally contains adequate zinc to meet the requirement for infants up to 4 to 6 months of age. Zinc deficiency can lead to dermatitis, alopecia, decreased growth, and impaired immune function. The disorder shows autosomal dominant inheritance with incomplete penetrance. {ECO:0000269|PubMed:17065149, ECO:0000269|PubMed:22733820}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- 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
- 0.159
Intolerance Scores
- loftool
- 0.409
- rvis_EVS
- 0.11
- rvis_percentile_EVS
- 61.73
Haploinsufficiency Scores
- pHI
- 0.105
- hipred
- Y
- hipred_score
- 0.570
- ghis
- 0.443
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.237
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc30a2
- Phenotype
- hematopoietic system phenotype; immune system 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); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- response to zinc ion;regulation of sequestering of zinc ion;positive regulation of sequestering of zinc ion;zinc ion transmembrane transport
- Cellular component
- cytoplasm;lysosomal membrane;late endosome;plasma membrane;integral component of membrane;intracellular membrane-bounded organelle
- Molecular function
- zinc ion transmembrane transporter activity;protein binding