SLC11A1
solute carrier family 11 member 1, the group of Solute carrier family 11
Basic information
Region (hg38): 2:218382029-218396894
Previous symbols: [ "LSH", "NRAMP", "NRAMP1" ]
Links
Phenotypes
GenCC
Source:
- cystic fibrosis (Supportive), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (93 variants)
- not_provided (15 variants)
- SLC11A1-related_disorder (8 variants)
- Mycobacterium_tuberculosis,_susceptibility_to (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC11A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000578.4. 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 | 7 | |||||
| missense | 86 | 10 | 100 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 86 | 15 | 6 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC11A1 | protein_coding | protein_coding | ENST00000233202 | 15 | 14866 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.55e-19 | 0.00294 | 125643 | 1 | 104 | 125748 | 0.000418 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.502 | 323 | 349 | 0.924 | 0.0000215 | 3513 |
| Missense in Polyphen | 124 | 136.64 | 0.90748 | 1391 | ||
| Synonymous | 0.0825 | 154 | 155 | 0.992 | 0.0000108 | 1157 |
| Loss of Function | 0.0345 | 29 | 29.2 | 0.993 | 0.00000157 | 290 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00189 | 0.00187 |
| Ashkenazi Jewish | 0.000199 | 0.000198 |
| East Asian | 0.000732 | 0.000707 |
| Finnish | 0.000140 | 0.000139 |
| European (Non-Finnish) | 0.000233 | 0.000229 |
| Middle Eastern | 0.000732 | 0.000707 |
| South Asian | 0.000398 | 0.000392 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Divalent transition metal (iron and manganese) transporter involved in iron metabolism and host resistance to certain pathogens. Macrophage-specific membrane transport function. Controls natural resistance to infection with intracellular parasites. Pathogen resistance involves sequestration of Fe(2+) and Mn(2+), cofactors of both prokaryotic and eukaryotic catalases and superoxide dismutases, not only to protect the macrophage against its own generation of reactive oxygen species, but to deny the cations to the pathogen for synthesis of its protective enzymes.;
- Pathway
- Lysosome - Homo sapiens (human);Ion influx/efflux at host-pathogen interface;Neutrophil degranulation;ROS, RNS production in phagocytes;Antimicrobial peptides;Innate Immune System;Immune System;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Metal ion SLC transporters;Validated targets of C-MYC transcriptional repression
(Consensus)
Recessive Scores
- pRec
- 0.339
Intolerance Scores
- loftool
- 0.911
- rvis_EVS
- -0.51
- rvis_percentile_EVS
- 21.77
Haploinsufficiency Scores
- pHI
- 0.123
- hipred
- N
- hipred_score
- 0.177
- ghis
- 0.618
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.195
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc11a1
- Phenotype
- immune system phenotype; digestive/alimentary 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; neoplasm;
Gene ontology
- Biological process
- negative regulation of cytokine production;positive regulation of cytokine production;T cell proliferation involved in immune response;T cell cytokine production;positive regulation of dendritic cell antigen processing and presentation;positive regulation of T-helper 1 type immune response;iron ion transport;manganese ion transport;cellular cadmium ion homeostasis;cellular iron ion homeostasis;phagocytosis;inflammatory response;vacuolar acidification;response to bacterium;positive regulation of gene expression;nitrite transport;antimicrobial humoral response;activation of protein kinase activity;response to lipopolysaccharide;interleukin-2 production;interleukin-3 production;positive regulation of interferon-gamma production;response to interferon-gamma;wound healing;macrophage activation;defense response to bacterium;defense response to protozoan;neutrophil degranulation;MHC class II biosynthetic process;cell redox homeostasis;respiratory burst;positive regulation of transcription by RNA polymerase II;antigen processing and presentation of peptide antigen;mRNA stabilization;positive regulation of phagocytosis;defense response to Gram-negative bacterium;iron ion homeostasis;multicellular organismal iron ion homeostasis;cadmium ion transmembrane transport;divalent metal ion export;manganese ion transmembrane transport;L-arginine transport
- Cellular component
- lysosome;late endosome;plasma membrane;integral component of plasma membrane;phagocytic vesicle membrane;late endosome membrane;tertiary granule membrane;ficolin-1-rich granule membrane
- Molecular function
- manganese ion transmembrane transporter activity;cadmium ion transmembrane transporter activity;protein homodimerization activity;transition metal ion transmembrane transporter activity;metal ion:proton antiporter activity