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SLC41A3 solute carrier family 41 member 3 [ Homo sapiens (human) ]

Gene ID: 54946, updated on 25-Nov-2025
Official Symbol
SLC41A3provided by HGNC
Official Full Name
solute carrier family 41 member 3provided by HGNC
Primary source
HGNC:HGNC:31046
See related
Ensembl:ENSG00000114544 MIM:610803; AllianceGenome:HGNC:31046
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SLC41A1-L2
Summary
Enables magnesium:sodium antiporter activity. Involved in mitochondrial magnesium ion transmembrane transport. Located in mitochondrial inner membrane and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
Expression
Ubiquitous expression in testis (RPKM 23.3), ovary (RPKM 19.3) and 25 other tissues See more
Orthologs
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See SLC41A3 in Genome Data Viewer
Location:
3q21.2-q21.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (126006357..126101520, complement)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (128738761..128834029, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (125725200..125820363, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ALG1 like 1, pseudogene Neighboring gene FBRSL1 pseudogene 1 Neighboring gene rhophilin associated tail protein 1B Neighboring gene ReSE screen-validated silencer GRCh37_chr3:125736296-125736478 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:125740258-125741040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125744116-125744616 Neighboring gene uncharacterized LOC124909425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125777675-125778174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14672 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14673 Neighboring gene ALDH1L1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125822083-125822904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125831607-125832121 Neighboring gene aldehyde dehydrogenase 1 family member L1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125847779-125848549 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125850681-125851498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125855703-125856203 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125876969-125877469 Neighboring gene uncharacterized LOC105374083 Neighboring gene RNA, U1 small nuclear 30, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125899089-125899844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125899845-125900598 Neighboring gene ALDH1L1 antisense RNA 2 Neighboring gene Sharpr-MPRA regulatory region 2719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20437 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:125926972-125928171

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. SLC41A3 Exhibits as a Carcinoma Biomarker and Promoter in Liver Hepatocellular Carcinoma. Chang Q, et al. Comput Math Methods Med, 2021. PMID 34819993, Free PMC Article
  2. Solute carrier 41A3 encodes for a mitochondrial Mg(2+) efflux system. Mastrototaro L, et al. Sci Rep, 2016 Jun 15. PMID 27302215, Free PMC Article
  3. The human solute carrier SLC41A1 belongs to a novel eukaryotic subfamily with homology to prokaryotic MgtE Mg2+ transporters. Wabakken T, et al. Biochem Biophys Res Commun, 2003 Jul 4. PMID 12810078
  4. Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. Virok DP, et al. J Proteome Res, 2011 Apr 1. PMID 21244100
  5. FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane. Ceccarelli DF, et al. Structure, 2019 Jun 4. PMID 31056421, Free PMC Article

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

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

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ20473

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables magnesium ion transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
enables magnesium:sodium antiporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables monoatomic cation transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in mitochondrial magnesium ion transmembrane transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in monoatomic cation transport IEA
Inferred from Electronic Annotation
more info
  
involved_in monoatomic ion transport IEA
Inferred from Electronic Annotation
more info
  
involved_in sodium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in mitochondrial inner membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial inner membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  
Preferred Names
solute carrier family 41 member 3
Names
SLC41A1-like 2

NEW Try the new Transcript table

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.

mRNA and Protein(s)

  1. NM_001008485.2 → NP_001008485.2  solute carrier family 41 member 3 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC079848, AC092903, AC117422
    Consensus CDS
    CCDS33843.1
    UniProtKB/Swiss-Prot
    A6ND60, B3KSD9, B7Z4Y2, C9JE96, E7ENY4, Q8N342, Q8NB27, Q96GZ6, Q9H9I6, Q9HAB1, Q9NX30
    Related
    ENSP00000326070.6, ENST00000315891.10
    Conserved Domains (1) summary
    pfam01769
    Location:319 → 456
    MgtE; Divalent cation transporter

  2. NM_001008486.2 → NP_001008486.2  solute carrier family 41 member 3 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an in-frame coding exon and uses alternate splicing in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 3) with a unique C-terminus.
    Source sequence(s)
    AC079848, AC092903, AC117422
    Consensus CDS
    CCDS33842.1
    Related
    ENSP00000264471.6, ENST00000346785.9
    Conserved Domains (1) summary
    pfam01769
    Location:283 → 420
    MgtE; Divalent cation transporter

  3. NM_001008487.2 → NP_001008487.1  solute carrier family 41 member 3 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) utilizes an alternate 5' coding exon, compared to variant 1, resulting in the shortest protein (isoform 4) that has a unique N-terminus compared to isoform 1.
    Source sequence(s)
    AC092903, AC117422
    Consensus CDS
    CCDS33844.1
    UniProtKB/Swiss-Prot
    Q96GZ6
    Related
    ENSP00000373092.2, ENST00000383598.6
    Conserved Domains (1) summary
    pfam01769
    Location:80 → 211
    MgtE; Divalent cation transporter

  4. NM_001164475.2 → NP_001157947.1  solute carrier family 41 member 3 isoform 5

    See identical proteins and their annotated locations for NP_001157947.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' and 3' UTRs and coding sequences compared to variant 1. The resulting isoform (5) is shorter at the N-terminus and has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC079848, AC092903, AC117422
    Consensus CDS
    CCDS54635.1
    UniProtKB/Swiss-Prot
    Q96GZ6
    Related
    ENSP00000427409.1, ENST00000508835.5
    Conserved Domains (1) summary
    pfam01769
    Location:1 → 121
    MgtE; Divalent cation transporter

  5. NM_017836.4 → NP_060306.4  solute carrier family 41 member 3 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses alternate splicing in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 2) with a unique C-terminus.
    Source sequence(s)
    AC079848, AC092903, AC117422
    Consensus CDS
    CCDS43144.1
    Related
    ENSP00000353533.4, ENST00000360370.9
    Conserved Domains (1) summary
    pfam01769
    Location:106 → 238
    MgtE; Divalent cation transporter

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    126006357..126101520 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005247563.3 → XP_005247620.1  solute carrier family 41 member 3 isoform X2

    See identical proteins and their annotated locations for XP_005247620.1

    UniProtKB/Swiss-Prot
    A6ND60, B3KSD9, B7Z4Y2, C9JE96, E7ENY4, Q8N342, Q8NB27, Q96GZ6, Q9H9I6, Q9HAB1, Q9NX30
    Conserved Domains (1) summary
    pfam01769
    Location:319 → 456
    MgtE; Divalent cation transporter

  2. XM_017006707.2 → XP_016862196.1  solute carrier family 41 member 3 isoform X5

    UniProtKB/Swiss-Prot
    Q96GZ6
    Conserved Domains (1) summary
    pfam01769
    Location:106 → 238
    MgtE; Divalent cation transporter

  3. XM_047448404.1 → XP_047304360.1  solute carrier family 41 member 3 isoform X1

  4. XM_017006708.1 → XP_016862197.1  solute carrier family 41 member 3 isoform X9

    Related
    ENSP00000580187.1, ENST00000910128.1

  5. XM_005247559.1 → XP_005247616.1  solute carrier family 41 member 3 isoform X1

    See identical proteins and their annotated locations for XP_005247616.1

    Conserved Domains (1) summary
    pfam01769
    Location:334 → 471
    MgtE; Divalent cation transporter

  6. XM_005247564.1 → XP_005247621.1  solute carrier family 41 member 3 isoform X3

    Related
    ENSP00000617493.1, ENST00000947434.1
    Conserved Domains (1) summary
    pfam01769
    Location:106 → 252
    MgtE; Divalent cation transporter

  7. XM_047448409.1 → XP_047304365.1  solute carrier family 41 member 3 isoform X9

  8. XM_006713681.4 → XP_006713744.1  solute carrier family 41 member 3 isoform X2

    See identical proteins and their annotated locations for XP_006713744.1

    UniProtKB/Swiss-Prot
    A6ND60, B3KSD9, B7Z4Y2, C9JE96, E7ENY4, Q8N342, Q8NB27, Q96GZ6, Q9H9I6, Q9HAB1, Q9NX30
    Conserved Domains (1) summary
    pfam01769
    Location:319 → 456
    MgtE; Divalent cation transporter

  9. XM_024453609.2 → XP_024309377.1  solute carrier family 41 member 3 isoform X5

    Related
    ENSP00000580185.1, ENST00000910126.1
    Conserved Domains (1) summary
    pfam01769
    Location:106 → 238
    MgtE; Divalent cation transporter

  10. XM_047448405.1 → XP_047304361.1  solute carrier family 41 member 3 isoform X1

  11. XM_047448406.1 → XP_047304362.1  solute carrier family 41 member 3 isoform X3

  12. XM_017006706.2 → XP_016862195.1  solute carrier family 41 member 3 isoform X5

    UniProtKB/Swiss-Prot
    Q96GZ6
    Related
    ENSP00000580188.1, ENST00000910129.1
    Conserved Domains (1) summary
    pfam01769
    Location:106 → 238
    MgtE; Divalent cation transporter

  13. XM_005247562.1 → XP_005247619.1  solute carrier family 41 member 3 isoform X2

    See identical proteins and their annotated locations for XP_005247619.1

    UniProtKB/Swiss-Prot
    A6ND60, B3KSD9, B7Z4Y2, C9JE96, E7ENY4, Q8N342, Q8NB27, Q96GZ6, Q9H9I6, Q9HAB1, Q9NX30
    Conserved Domains (1) summary
    pfam01769
    Location:319 → 456
    MgtE; Divalent cation transporter

  14. XM_024453610.1 → XP_024309378.1  solute carrier family 41 member 3 isoform X8

    Conserved Domains (1) summary
    pfam01769
    Location:283 → 420
    MgtE; Divalent cation transporter

  15. XM_017006709.1 → XP_016862198.1  solute carrier family 41 member 3 isoform X9

    Related
    ENSP00000617496.1, ENST00000947437.1

  16. XM_047448407.1 → XP_047304363.1  solute carrier family 41 member 3 isoform X3

    Related
    ENSP00000617497.1, ENST00000947438.1

  17. XM_017006705.2 → XP_016862194.1  solute carrier family 41 member 3 isoform X1

    Conserved Domains (1) summary
    pfam01769
    Location:334 → 471
    MgtE; Divalent cation transporter

  18. XM_047448411.1 → XP_047304367.1  solute carrier family 41 member 3 isoform X10

  19. XM_047448412.1 → XP_047304368.1  solute carrier family 41 member 3 isoform X11

  20. XM_005247565.3 → XP_005247622.1  solute carrier family 41 member 3 isoform X6

    Conserved Domains (1) summary
    pfam01769
    Location:293 → 430
    MgtE; Divalent cation transporter

  21. XM_011512945.2 → XP_011511247.1  solute carrier family 41 member 3 isoform X4

    Conserved Domains (1) summary
    pfam01769
    Location:308 → 445
    MgtE; Divalent cation transporter

  22. XM_047448408.1 → XP_047304364.1  solute carrier family 41 member 3 isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    128738761..128834029 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347017.1 → XP_054202992.1  solute carrier family 41 member 3 isoform X5

  2. XM_054347011.1 → XP_054202986.1  solute carrier family 41 member 3 isoform X2

  3. XM_054347007.1 → XP_054202982.1  solute carrier family 41 member 3 isoform X1

  4. XM_054347021.1 → XP_054202996.1  solute carrier family 41 member 3 isoform X9

  5. XM_054347006.1 → XP_054202981.1  solute carrier family 41 member 3 isoform X1

  6. XM_054347012.1 → XP_054202987.1  solute carrier family 41 member 3 isoform X3

  7. XM_054347016.1 → XP_054202991.1  solute carrier family 41 member 3 isoform X5

  8. XM_054347009.1 → XP_054202984.1  solute carrier family 41 member 3 isoform X2

  9. XM_054347013.1 → XP_054202988.1  solute carrier family 41 member 3 isoform X3

  10. XM_054347022.1 → XP_054202997.1  solute carrier family 41 member 3 isoform X9

  11. XM_054347010.1 → XP_054202985.1  solute carrier family 41 member 3 isoform X2

  12. XM_054347020.1 → XP_054202995.1  solute carrier family 41 member 3 isoform X8

  13. XM_054347023.1 → XP_054202998.1  solute carrier family 41 member 3 isoform X9

  14. XM_054347014.1 → XP_054202989.1  solute carrier family 41 member 3 isoform X3

  15. XM_054347008.1 → XP_054202983.1  solute carrier family 41 member 3 isoform X1

  16. XM_054347024.1 → XP_054202999.1  solute carrier family 41 member 3 isoform X10

  17. XM_054347025.1 → XP_054203000.1  solute carrier family 41 member 3 isoform X11

  18. XM_054347018.1 → XP_054202993.1  solute carrier family 41 member 3 isoform X6

  19. XM_054347015.1 → XP_054202990.1  solute carrier family 41 member 3 isoform X4

  20. XM_054347019.1 → XP_054202994.1  solute carrier family 41 member 3 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96GZ6.2 GenPept UniProtKB/Swiss-Prot:Q96GZ6

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