SLC11A1

solute carrier family 11 member 1, the group of Solute carrier family 11

Basic information

Region (hg38): 2:218382028-218396894

Previous symbols: [ "LSH", "NRAMP", "NRAMP1" ]

Links

ENSG00000018280 ∙ NCBI:6556 ∙ OMIM:600266 ∙ HGNC:10907 ∙ Uniprot:P49279 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC11A1 gene.

• Inborn genetic diseases (42 variants)
• not provided (10 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			40	4	2	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding						0
Total	0	0	40	6	3

Variants in SLC11A1

This is a list of pathogenic ClinVar variants found in the SLC11A1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-218382986-G-A		not specified	Likely benign (Mar 20, 2023)
2-218382988-G-A			Likely benign (Dec 01, 2023)
2-218383014-C-T		not specified	Uncertain significance (Aug 12, 2021)
2-218383023-C-T		not specified	Uncertain significance (Jan 31, 2024)
2-218383067-C-T		SLC11A1-related disorder	Benign (Jan 28, 2020)
2-218383095-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-218383101-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-218384247-C-T		not specified	Uncertain significance (Nov 18, 2022)
2-218384290-C-T		Mycobacterium tuberculosis, susceptibility to infection by	risk factor (Aug 23, 2005)
2-218384312-G-C		not specified	Uncertain significance (Jun 06, 2023)
2-218384348-G-A		not specified	Uncertain significance (Dec 17, 2023)
2-218385169-C-T		not specified	Uncertain significance (Jun 22, 2021)
2-218385180-G-T		not specified	Uncertain significance (Feb 22, 2024)
2-218385197-A-T			Likely benign (Aug 08, 2018)
2-218385240-G-A		not specified	Uncertain significance (Mar 15, 2023)
2-218385246-T-A		not specified	Uncertain significance (Jan 30, 2024)
2-218386647-G-A		not specified	Uncertain significance (Feb 16, 2023)
2-218386674-A-T		not specified	Uncertain significance (Jan 20, 2023)
2-218386686-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-218386714-T-C		not specified	Uncertain significance (Aug 02, 2021)
2-218387156-T-G			Benign (Dec 04, 2017)
2-218387164-C-A		not specified	Uncertain significance (Jun 24, 2022)
2-218387181-C-T			Benign (Jun 18, 2018)
2-218387204-T-C		not specified	Uncertain significance (Dec 20, 2021)
2-218387217-C-G		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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