SLC39A10
Basic information
Region (hg38): 2:195575977-195737702
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (73 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020342.3. 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 | 65 | 73 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 65 | 8 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC39A10 | protein_coding | protein_coding | ENST00000409086 | 9 | 161726 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.993 | 0.00730 | 125720 | 0 | 3 | 125723 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.95 | 334 | 451 | 0.741 | 0.0000224 | 5605 |
| Missense in Polyphen | 94 | 177.21 | 0.53045 | 2261 | ||
| Synonymous | -0.0133 | 158 | 158 | 1.00 | 0.00000795 | 1508 |
| Loss of Function | 4.37 | 3 | 27.9 | 0.107 | 0.00000130 | 392 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000915 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May act as a zinc-influx transporter. {ECO:0000269|PubMed:17359283}.;
- Pathway
- Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis;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
- 0.115
Intolerance Scores
- loftool
- 0.139
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 42.16
Haploinsufficiency Scores
- pHI
- 0.855
- hipred
- Y
- hipred_score
- 0.654
- ghis
- 0.572
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.182
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc39a10
- 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; cellular phenotype; homeostasis/metabolism 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); hematopoietic system phenotype; immune system phenotype;
Zebrafish Information Network
- Gene name
- slc39a10
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- bent
Gene ontology
- Biological process
- negative regulation of B cell apoptotic process;cellular zinc ion homeostasis;positive regulation of B cell proliferation;positive regulation of B cell receptor signaling pathway;zinc ion import across plasma membrane;positive regulation of protein tyrosine phosphatase activity
- Cellular component
- integral component of plasma membrane
- Molecular function
- zinc ion transmembrane transporter activity