U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 123606, updated on 5-Mar-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
15q11.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (22786225..22829789)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (20458058..20501621)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Clinical and genetic characterization of NIPA1 mutations in a Taiwanese cohort with hereditary spastic paraplegia. Fang SY, et al. Ann Clin Transl Neurol, 2023 Mar. PMID 36607129, Free PMC Article
  2. Analysis of the GCG repeat length in NIPA1 gene in C9orf72-mediated ALS in a large Italian ALS cohort. Corrado L, et al. Neurol Sci, 2019 Dec. PMID 31286297
  3. Association of NIPA1 repeat expansions with amyotrophic lateral sclerosis in a large international cohort. Tazelaar GHP, et al. Neurobiol Aging, 2019 Feb. PMID 30342764, Free PMC Article
  4. Pure hereditary spastic paraplegia due to a de novo mutation in the NIPA1 gene. Arkadir D, et al. Eur J Neurol, 2014. PMID 25133278, Free PMC Article
  5. Recurrent de novo c.316G>A mutation in NIPA1 hotspot. Hedera P. J Neurol Sci, 2013 Dec 15. PMID 24075313

See all (39) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. NIPA1 polyalanine repeat expansions are a common risk factor for ALS and modulate disease course
    Title: NIPA1 polyalanine repeat expansions are associated with amyotrophic lateral sclerosis.
Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
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)

Go to the top of the page Help

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.

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_2023_10

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous