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

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: mouse all
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Genomic context

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_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:487172

D15S912 (e-PCR)
- UniSTS:62293

G19907 (e-PCR)
- UniSTS:36188

A002B45 (e-PCR)
- UniSTS:36189

RH11248 (e-PCR)
- UniSTS:49279

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

NG_009056.1 RefSeqGene

Range

5420..48565

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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