NIPA1 non imprinted in Prader-Willi/Angelman syndrome 1 [Homo sapiens] - Gene

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Summary

Official Symbol: NIPA1provided by HGNC
Official Full Name: non imprinted in Prader-Willi/Angelman syndrome 1provided by HGNC
Primary source: HGNC:17043
See related: Ensembl:ENSG00000170113; HPRD:10487; MIM:608145; Vega:OTTHUMG00000129099
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; MGC35570; MGC102724
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]

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Genomic context

Location :: 15q11.2

Sequence :: Chromosome: 15; NC_000015.9 (23043279..23086843, complement)

See NIPA1 in Epigenomics, MapViewer

Chromosome 15 - NC_000015.9 Genomic Context describing neighboring genes

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Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

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Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

Epilepsy might be more common in spastic paraplegia type 6 than in other forms of Hereditary spastic paraplegia because of a genetic risk factor closely linked to NIPA1.
Title: NIPA1 mutation in complex hereditary spastic paraplegia with epilepsy.
One heterozygous missense mutation of NIPA1 was identified in a complicated form of hereditary spastic paraplegia type 6 family with peripheral nerves disease
Title: Expansion of the phenotypic spectrum of SPG6 caused by mutation in NIPA1.
a genome-wide association study of amyotrophic lateral sclerosis identified the NIPA1 locus as a candidate for more in-depth studies
Title: A large genome scan for rare CNVs in amyotrophic lateral sclerosis.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: A large genome scan for rare CNVs in amyotrophic lateral sclerosis.
The hereditary spastic paraplegia proteins NIPA1, spastin and spartin inhibit BMP signalling by promoting BMP receptors degradation.
Title: The hereditary spastic paraplegia proteins NIPA1, spastin and spartin are inhibitors of mammalian BMP signalling.
We propose that Hereditary spastic paraplegia-associated mutations in NIPA1 lead to cellular and functional deficits through a gain-of-function mechanism supporting the endoplasmic reticulum accumulation of toxic NIPA1 proteins.
Title: Hereditary spastic paraplegia-associated mutations in the NIPA1 gene and its Caenorhabditis elegans homolog trigger neural degeneration in vitro and in vivo through a gain-of-function mechanism.
utations in the NIPA1 gene cause autosomal dominant hereditary spastic paraplegia and further demonstrates genotype-phenotype correlations in SPG6
Title: Clinical and genetic study of SPG6 mutation in a Chinese family with hereditary spastic paraplegia.
Observational study of gene-disease association. (HuGE Navigator)
Title: Comprehensive copy number variant (CNV) analysis of neuronal pathways genes in psychiatric disorders identifies rare variants within patients.
Amino acid substitution mutations implicated in a family with autosomal dominant spastic paraplegia.
Title: NIPA1 (SPG6) mutations are a rare cause of autosomal dominant spastic paraplegia in Europe.
discovery of a dominant negative mutation in the NIPA1 gene in a kindred with autosomal dominant hereditary spastic paraplegia
Title: NIPA1 gene mutations cause autosomal dominant hereditary spastic paraplegia (SPG6).

Submit: New GeneRIF Correction See all (14)

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Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

Spastic paraplegia 6, autosomal dominant

MIM: 600363

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Process	Evidence Code	Pubs
cell death	IEA Inferred from Electronic Annotation more info
ion transport	IEA Inferred from Electronic Annotation more info
magnesium ion transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
early endosome	IEA Inferred from Electronic Annotation more info
integral to membrane	IEA Inferred from Electronic Annotation more info
plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

Preferred Names: magnesium transporter NIPA1

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

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NCBI Reference Sequences (RefSeq)

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

5001..48565

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

CCDS45190.1

UniProtKB/Swiss-Prot

Q7RTP0

UniProtKB/TrEMBL

Q8TAY1

Related

ENSP00000453722, OTTHUMP00000247182, ENST00000561183, OTTHUMT00000415892

Conserved Domains (1) summary

pfam05653
Location:1 – 243
Blast Score: 501

Mg_trans_NIPA; Magnesium transporter NIPA
NM_144599.4 → NP_653200.2 magnesium transporter NIPA1 isoform 1

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

CCDS10011.1

UniProtKB/Swiss-Prot

Q7RTP0

Related

ENSP00000337452, OTTHUMP00000159352, ENST00000337435, OTTHUMT00000251135

Conserved Domains (1) summary

pfam05653
Location:45 – 318
Blast Score: 579

Mg_trans_NIPA; Magnesium transporter NIPA

RefSeqs of Annotated Genomes: Build 37.3

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

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000015.9 Reference GRCh37.p5 Primary Assembly

Range

23043279..23086843, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000147.1 Alternate HuRef

Range

1354946..1373627, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

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Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AC011767.12 (70054..113211)	None
genomic	CH471258.1	EAW65549.1
		EAW65550.1
		EAW65551.1
genomic	CQ834740.1	CAH05585.1
mRNA	AB089319.1	BAC67707.1
mRNA	AK057846.1	None
mRNA	AK314073.1	BAG36773.1
mRNA	BC025678.1	AAH25678.2
mRNA	BC103705.1	AAI03706.1
mRNA	BK001020.1	DAA01477.1
mRNA	BX648722.1	CAI45979.2
other-genetic	BC156247.1	AAI56248.1
other-genetic	BC172484.1	AAI72484.1
other-genetic	DQ891252.2	ABM82178.1
other-genetic	DQ894438.2	ABM85364.1

Protein Accession	Links
Protein Accession	GenPept Link	UniProtKB Link
Q3SYP4	GenPept	UniProtKB/TrEMBL:Q3SYP4
Q7RTP0.1	GenPept	UniProtKB/Swiss-Prot:Q7RTP0
Q8TAY1	GenPept	UniProtKB/TrEMBL:Q8TAY1