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    NIPA1 NIPA magnesium transporter 1 [ Homo sapiens (human) ]

    Gene ID: 123606, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NIPA1provided by HGNC
    Official Full Name
    NIPA magnesium transporter 1provided by HGNC
    Primary source
    HGNC:HGNC:17043
    See related
    Ensembl:ENSG00000170113 MIM:608145; AllianceGenome:HGNC:17043
    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
    FSP3; SPG6; SLC57A1
    Summary
    This gene encodes a magnesium transporter that associates with early endosomes and the cell surface in a variety of neuronal and epithelial cells. This protein may play a role in nervous system development and maintenance. Multiple transcript variants encoding different isoforms have been found for this gene. Mutations in this gene have been associated with autosomal dominant spastic paraplegia 6. [provided by RefSeq, Nov 2008]
    Expression
    Ubiquitous expression in brain (RPKM 16.6), thyroid (RPKM 6.7) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NIPA1 in Genome Data Viewer
    Location:
    15q11.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (22786225..22829789)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (20458058..20501621)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (23043279..23086843, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene C-X9-C motif containing 2 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:23106710-23107210 Neighboring gene uncharacterized LOC283683 Neighboring gene Sharpr-MPRA regulatory region 3977 Neighboring gene golgin subfamily A member 6-like protein 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:23086519-23086752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6260 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:23080143-23080643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9155 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:23045427-23046179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9158 Neighboring gene NIPA magnesium transporter 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:22999149-22999824 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:22990202-22991401 Neighboring gene cytoplasmic FMR1 interacting protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:22981163-22981662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:22980661-22981162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:22925256-22925940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:22905531-22906030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:22896003-22896502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:22895501-22896002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:22893404-22894371 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:22892435-22893403 Neighboring gene tubulin gamma complex component 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:22859095-22860005

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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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    Related articles in PubMed

    1. LncRNA NIPA1-SO confers atherosclerotic protection by suppressing the transmembrane protein NIPA1. Jiang M, et al. J Adv Res, 2023 Dec. PMID 36736696, Free PMC Article
    2. Autosomal dominant familial spastic paraplegia: tight linkage to chromosome 15q. Fink JK, et al. Am J Hum Genet, 1995 Jan. PMID 7825577, Free PMC Article
    3. Hereditary spastic paraplegia linked to chromosome 15q: Analysis of candidate genes. Fink JK, et al. Neurology, 1996 Mar. PMID 8618696
    4. Analysis of mRNA with microsomal fractionation using a SAGE-based DNA microarray system facilitates identification of the genes encoding secretory proteins. Toyoda N, et al. Genome Res, 2003 Jul. PMID 12805275, Free PMC Article
    5. NIPA1 gene mutations cause autosomal dominant hereditary spastic paraplegia (SPG6). Rainier S, et al. Am J Hum Genet, 2003 Oct. PMID 14508710, Free PMC Article

    See all (41) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Investigating Repeat Expansions in NIPA1, NOP56, and NOTCH2NLC Genes: A Closer Look at Amyotrophic Lateral Sclerosis Patients from Southern Italy.
      Title: Investigating Repeat Expansions in NIPA1, NOP56, and NOTCH2NLC Genes: A Closer Look at Amyotrophic Lateral Sclerosis Patients from Southern Italy.
    2. LncRNA NIPA1-SO confers atherosclerotic protection by suppressing the transmembrane protein NIPA1.
      Title: LncRNA NIPA1-SO confers atherosclerotic protection by suppressing the transmembrane protein NIPA1.
    3. Clinical and genetic characterization of NIPA1 mutations in a Taiwanese cohort with hereditary spastic paraplegia.
      Title: Clinical and genetic characterization of NIPA1 mutations in a Taiwanese cohort with hereditary spastic paraplegia.
    4. No role of NIPA1 repeat length as a modifier of the C9orf72 ALS disease risk.
      Title: Analysis of the GCG repeat length in NIPA1 gene in C9orf72-mediated ALS in a large Italian ALS cohort.
    5. There is an evidence for an association of an expanded polyalanine repeat in NIPA1 and ALS.
      Title: Association of NIPA1 repeat expansions with amyotrophic lateral sclerosis in a large international cohort.
    6. we employed an shRNA-encoding lentivirus system to inhibit SPG6 expression in AML cells including NB4 and MV4-11cells. Knockdown expression of SPG6 resulted in decreased cell growth and elevated apoptosis of these leukemia cells. Notably, SPG6 deficiency resulted in higher BMPR2 expression indicating that BMPR2 signaling contributes to AML pathogenesis.
      Title: SPG6 supports development of acute myeloid leukemia by regulating BMPR2-Smad-Bcl-2/Bcl-xl signaling.
    7. This study showed that the mutations of were detected in SPG11, ATL1, NIPA1, and ABCD1 in patient with hereditary spastic paraplegia.
      Title: Genetic background of the hereditary spastic paraplegia phenotypes in Hungary - An analysis of 58 probands.
    8. NIPA1 repeat expansion in the context of a C9orf72 repeat expansion would drive toward a motor neuron disease phenotype.
      Title: Large-scale screening in sporadic amyotrophic lateral sclerosis identifies genetic modifiers in C9orf72 repeat carriers.
    9. We report here a family with a pure form of Hereditary spastic paraplegia due to a de novo transition mutation in the NIPA1 gene.
      Title: Pure hereditary spastic paraplegia due to a de novo mutation in the NIPA1 gene.
    10. study reports direct evidence of de novo c.316G>A mutation in the same hotspot of the gene in two unrelated patients who had otherwise a prototypical NIPA1-associated phenotype with a severe form of uncomplicated spastic paraplegia
      Title: Recurrent de novo c.316G>A mutation in NIPA1 hotspot.
    Submit: New GeneRIF Correction See all GeneRIFs (25)

    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
    Hereditary spastic paraplegia 6
    MedGen: C1838192 OMIM: 600363 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-04-04)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-04-04)

    ClinGen Genome Curation Page

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC35570, MGC102724

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables magnesium ion transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in magnesium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in magnesium ion transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transmembrane transport TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in early endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    magnesium transporter NIPA1
    Names
    non imprinted in Prader-Willi/Angelman syndrome 1
    non-imprinted in Prader-Willi/Angelman syndrome region protein 1
    spastic paraplegia 6 protein

    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

    1. NG_009056.1 RefSeqGene

      Range
      5420..48565
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001142275.1 → NP_001135747.1  magnesium transporter NIPA1 isoform 2

      See identical proteins and their annotated locations for NP_001135747.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate 5' exon and downstream start codon, compared to variant 1. The resulting protein (isoform 2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      BC025678, BK001020
      Consensus CDS
      CCDS73692.1
      UniProtKB/TrEMBL
      Q8TAY1
      Related
      ENSP00000453722.1, ENST00000561183.5
      Conserved Domains (1) summary
      cl23754
      Location:1 → 238
      EamA; EamA-like transporter family

    2. NM_144599.5 → NP_653200.2  magnesium transporter NIPA1 isoform 1

      See identical proteins and their annotated locations for NP_653200.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK314073, BK001020
      Consensus CDS
      CCDS73691.1
      UniProtKB/Swiss-Prot
      B2RA76, Q5HYA9, Q7KZB0, Q7RTP0, Q86XW4
      UniProtKB/TrEMBL
      Q8TAY1
      Related
      ENSP00000337452.4, ENST00000337435.9
      Conserved Domains (1) summary
      cl23754
      Location:31 → 313
      EamA; EamA-like transporter family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      22786225..22829789
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_021160017.1 Reference GRCh38.p14 PATCHES

      Range
      3680257..3723836
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      20458058..20501621
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7RTP0.1 GenPept UniProtKB/Swiss-Prot:Q7RTP0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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