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

Gene ID: 123606, updated on 17-Jun-2024

Summary

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
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Genomic context

See NIPA1 in Genome Data Viewer
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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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_001142275.1NP_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:1238
    EamA; EamA-like transporter family
  2. NM_144599.5NP_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:31313
    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)