SLC11A1 solute carrier family 11 member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC11A1provided by HGNC
Official Full Name: solute carrier family 11 member 1provided by HGNC
Primary source: HGNC:HGNC:10907
See related: Ensembl:ENSG00000018280 MIM:600266; AllianceGenome:HGNC:10907
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LSH; NRAMP; NRAMP1
Summary: This gene is a member of the solute carrier family 11 (proton-coupled divalent metal ion transporters) family and encodes a multi-pass membrane protein. The protein functions as a divalent transition metal (iron and manganese) transporter involved in iron metabolism and host resistance to certain pathogens. Mutations in this gene have been associated with susceptibility to infectious diseases such as tuberculosis and leprosy, and inflammatory diseases such as rheumatoid arthritis and Crohn disease. Alternatively spliced variants that encode different protein isoforms have been described but the full-length nature of only one has been determined. [provided by RefSeq, Jul 2008]
Expression: Biased expression in lung (RPKM 10.4), appendix (RPKM 8.8) and 7 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q35

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (218382273..218396894)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (218868403..218883023)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (219246996..219261617)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Systemic assessment of solute carrier family 11-member A1 (rs17235409) gene polymorphism and Mycobacterium Tuberculosis Risk in Asian and caucasian population: A comprehensive updated meta-analysis.
Title: Systemic assessment of solute carrier family 11-member A1 (rs17235409) gene polymorphism and Mycobacterium Tuberculosis Risk in Asian and caucasian population: A comprehensive updated meta-analysis.
The expression of Nramp1 modulates the uptake of Mycobacterium tuberculosis by macrophages through alternating inflammatory responses.
Title: The expression of Nramp1 modulates the uptake of Mycobacterium tuberculosis by macrophages through alternating inflammatory responses.
Serum iron levels in tuberculosis patients and household contacts and its association with natural resistance-associated macrophage protein 1 polymorphism and expression.
Title: Serum iron levels in tuberculosis patients and household contacts and its association with natural resistance-associated macrophage protein 1 polymorphism and expression.
USP11-mediated LSH deubiquitination inhibits ferroptosis in colorectal cancer through epigenetic activation of CYP24A1.
Title: USP11-mediated LSH deubiquitination inhibits ferroptosis in colorectal cancer through epigenetic activation of CYP24A1.
Solute carrier family 11 member 1 genetic polymorphisms rs17235409 and rs3731865 associate with susceptibility to extremity post-traumatic osteomyelitis in a Chinese Han population.
Title: Solute carrier family 11 member 1 genetic polymorphisms rs17235409 and rs3731865 associate with susceptibility to extremity post-traumatic osteomyelitis in a Chinese Han population.
Association of SLC11A1 polymorphisms with anthropometric and biochemical parameters describing Type 2 Diabetes Mellitus.
Title: Association of SLC11A1 polymorphisms with anthropometric and biochemical parameters describing Type 2 Diabetes Mellitus.
SLC11A1 genetic variation and low expression may cause immune response impairment in TB patients.
Title: SLC11A1 genetic variation and low expression may cause immune response impairment in TB patients.
Polymorphisms of SLC11A1(NRAMP1) rs17235409 associated with and susceptibility to spinal tuberculosis in a southern Han Chinese population.
Title: Polymorphisms of SLC11A1(NRAMP1) rs17235409 associated with and susceptibility to spinal tuberculosis in a southern Han Chinese population.
Mutation analysis of seven SLC family transporters for early-onset Parkinson's disease in Chinese population.
Title: Mutation analysis of seven SLC family transporters for early-onset Parkinson's disease in Chinese population.
Association of genetic variants in autophagy-lysosome pathway genes with susceptibility and survival to prostate cancer.
Title: Association of genetic variants in autophagy-lysosome pathway genes with susceptibility and survival to prostate cancer.

Submit: New GeneRIF Correction See all GeneRIFs (147)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Buruli ulcer, susceptibility to MedGen: C1864868 OMIM: 610446 GeneReviews: Not available	Compare labs
Mycobacterium tuberculosis, susceptibility to MedGen: C1834752 OMIM: 607948 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

General gene information

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Markers

D11S2560 (e-PCR)
- UniSTS:37928

D8S2279 (e-PCR)
- UniSTS:473907

D22S1584 (e-PCR)
- UniSTS:473695

RH80764 (e-PCR)
- UniSTS:88945

D1S1425 (e-PCR)
- UniSTS:149621

SLC11A1-1 (e-PCR)
- UniSTS:513653

D11S3114 (e-PCR)
- UniSTS:152207

D2S2821 (e-PCR)
- UniSTS:52142

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cadmium ion transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables iron ion transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables iron ion transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables manganese ion transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables manganese ion transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables manganese ion transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables metal cation:proton antiporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables metal cation:proton antiporter activity	IDA Inferred from Direct Assay more info	PubMed
enables metal cation:proton antiporter activity	IGI Inferred from Genetic Interaction more info	PubMed
enables metal cation:proton antiporter activity	TAS Traceable Author Statement more info
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables transition metal ion transmembrane transporter activity	IGI Inferred from Genetic Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in L-arginine transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in MHC class II biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in T cell proliferation involved in immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in activation of protein kinase activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in antigen processing and presentation of peptide antigen	ISS Inferred from Sequence or Structural Similarity more info
involved_in antimicrobial humoral response	TAS Traceable Author Statement more info
involved_in cadmium ion transmembrane transport	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cell redox homeostasis	TAS Traceable Author Statement more info
involved_in cellular detoxification of cadmium ion	IGI Inferred from Genetic Interaction more info	PubMed
involved_in defense response to Gram-negative bacterium	ISS Inferred from Sequence or Structural Similarity more info
involved_in defense response to bacterium	ISS Inferred from Sequence or Structural Similarity more info
involved_in defense response to protozoan	ISS Inferred from Sequence or Structural Similarity more info
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular iron ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in iron ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in iron ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in iron ion transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA stabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in macrophage activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in manganese ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in manganese ion transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in manganese ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in manganese ion transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in metal ion transport	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in multicellular organismal-level iron ion homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in nitrite transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in phagocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of T-helper 1 type immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of dendritic cell antigen processing and presentation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phagocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within positive regulation of type II interferon production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of type II interferon production	ISS Inferred from Sequence or Structural Similarity more info
involved_in proton transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in respiratory burst	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to bacterium	IDA Inferred from Direct Assay more info	PubMed
involved_in response to lipopolysaccharide	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to type II interferon	ISS Inferred from Sequence or Structural Similarity more info
involved_in vacuolar acidification	ISS Inferred from Sequence or Structural Similarity more info
involved_in wound healing	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in ficolin-1-rich granule membrane	TAS Traceable Author Statement more info
located_in late endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in late endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in late endosome membrane	TAS Traceable Author Statement more info
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in lysosome	ISS Inferred from Sequence or Structural Similarity more info
is_active_in phagocytic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in phagocytic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in tertiary granule membrane	IDA Inferred from Direct Assay more info	PubMed
located_in tertiary granule membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: natural resistance-associated macrophage protein 1

Names: Leishmaniasis resistance; NRAMP 1; solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1; solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1; solute carrier family 11 (sodium/phosphate symporters), member 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_012128.1 RefSeqGene

Range

5245..19866

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000578.4 → NP_000569.3 natural resistance-associated macrophage protein 1

See identical proteins and their annotated locations for NP_000569.3

Status: REVIEWED

Source sequence(s)

AC021016, CA307182, DB284801, L32185

Consensus CDS

CCDS2415.1

UniProtKB/Swiss-Prot

C0H5Y3, P49279

UniProtKB/TrEMBL

B4E0J2

Related

ENSP00000233202.6, ENST00000233202.11

Conserved Domains (2) summary

TIGR01197
Location:56 → 456

nramp; NRAMP (natural resistance-associated macrophage protein) metal ion transporters

pfam01566
Location:78 → 463

Nramp; Natural resistance-associated macrophage protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

218382273..218396894

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005246793.5 → XP_005246850.1 natural resistance-associated macrophage protein 1 isoform X1

See identical proteins and their annotated locations for XP_005246850.1

UniProtKB/TrEMBL

B4E0J2

Conserved Domains (2) summary

TIGR01197
Location:1 → 389

nramp; NRAMP (natural resistance-associated macrophage protein) metal ion transporters

pfam01566
Location:11 → 396

Nramp; Natural resistance-associated macrophage protein
XM_006712711.5 → XP_006712774.1 natural resistance-associated macrophage protein 1 isoform X4

UniProtKB/TrEMBL

B4E0J2

Conserved Domains (2) summary

pfam01566
Location:1 → 314

Nramp; Natural resistance-associated macrophage protein

cl00456
Location:1 → 307

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_047445574.1 → XP_047301530.1 natural resistance-associated macrophage protein 1 isoform X3

UniProtKB/TrEMBL

B4DQ73, B9ZVN3
XM_047445575.1 → XP_047301531.1 natural resistance-associated macrophage protein 1 isoform X5
XM_017004766.3 → XP_016860255.1 natural resistance-associated macrophage protein 1 isoform X1

UniProtKB/TrEMBL

B4E0J2

Conserved Domains (2) summary

TIGR01197
Location:1 → 389

nramp; NRAMP (natural resistance-associated macrophage protein) metal ion transporters

pfam01566
Location:11 → 396

Nramp; Natural resistance-associated macrophage protein
XM_047445573.1 → XP_047301529.1 natural resistance-associated macrophage protein 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

218868403..218883023

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054343500.1 → XP_054199475.1 natural resistance-associated macrophage protein 1 isoform X1
XM_054343504.1 → XP_054199479.1 natural resistance-associated macrophage protein 1 isoform X4
XM_054343503.1 → XP_054199478.1 natural resistance-associated macrophage protein 1 isoform X3

UniProtKB/TrEMBL

B4DQ73, B9ZVN3
XM_054343505.1 → XP_054199480.1 natural resistance-associated macrophage protein 1 isoform X5
XM_054343501.1 → XP_054199476.1 natural resistance-associated macrophage protein 1 isoform X1
XM_054343502.1 → XP_054199477.1 natural resistance-associated macrophage protein 1 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001032220.1: Suppressed sequence

Description

NM_001032220.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.