Human Gene SPG7 (uc002fni.3) Description and Page Index
  Description: Homo sapiens spastic paraplegia 7 (pure and complicated autosomal recessive) (SPG7), nuclear gene encoding mitochondrial protein, transcript variant 2, mRNA.
RefSeq Summary (NM_199367): This gene encodes a mitochondrial metalloprotease protein that is a member of the AAA family. Members of this protein family share an ATPase domain and have roles in diverse cellular processes including membrane trafficking, intracellular motility, organelle biogenesis, protein folding, and proteolysis. Mutations in this gene cause autosomal recessive spastic paraplegia 7. Two transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Mar 2014].
Transcript (Including UTRs)
   Position: hg19 chr16:89,574,805-89,604,129 Size: 29,325 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr16:89,574,826-89,603,318 Size: 28,493 Coding Exon Count: 10 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:89,574,805-89,604,129)mRNA (may differ from genome)Protein (489 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SPG7
CDC HuGE Published Literature: SPG7
Positive Disease Associations: Hemoglobin A, Glycosylated , Lipoproteins, VLDL
Related Studies:
  1. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
  2. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
  3. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SPG7
Diseases sorted by gene-association score: spastic paraplegia 7, autosomal recessive* (1687), primary lateral sclerosis, adult, 1* (350), paraplegia (78), hereditary spastic paraplegia (18), orthostatic proteinuria (15), spasticity (13), spinocerebellar ataxia 28 (12), spastic ataxia (9), familial hypocalciuric hypercalcemia (9), troyer syndrome (9), chronic progressive external ophthalmoplegia (8), spastic paraplegia 4, autosomal dominant (8), spastic paraplegia 15, autosomal recessive (8), autosomal recessive cerebellar ataxia (7), hypoparathyroidism (7), spastic paraplegia 32, autosomal recessive (7), spastic paraplegia 11, autosomal recessive (7), spastic paraplegia 24, autosomal recessive (6), spastic paraplegia 49, autosomal recessive (6), hereditary ataxia (5), kbg syndrome (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 29.63 RPKM in Thyroid
Total median expression: 767.40 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -5.8021-0.276 Picture PostScript Text
3' UTR -316.22811-0.390 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00004 - ATPase family associated with various cellular activities (AAA)
PF06480 - FtsH Extracellular
PF07728 - AAA domain (dynein-related subfamily)

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q9UQ90-2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  BC036104 - Homo sapiens spastic paraplegia 7 (pure and complicated autosomal recessive), mRNA (cDNA clone MGC:33917 IMAGE:5274587), complete cds.
JD297126 - Sequence 278150 from Patent EP1572962.
Y16610 - Homo sapiens mRNA for paraplegin.
BC007692 - Homo sapiens spastic paraplegia 7, paraplegin (pure and complicated autosomal recessive), mRNA (cDNA clone IMAGE:3956605).
EU832769 - Synthetic construct Homo sapiens clone HAIB:100067798; DKFZo008A1233 spastic paraplegia 7 (pure and complicated autosomal recessive) protein (SPG7) gene, encodes complete protein.
GQ129312 - Synthetic construct Homo sapiens clone HAIB:100068459; DKFZo004A1234 spastic paraplegia 7 (pure and complicated autosomal recessive) protein (SPG7) gene, partial cds.
KJ901759 - Synthetic construct Homo sapiens clone ccsbBroadEn_11153 SPG7 gene, encodes complete protein.
KR710030 - Synthetic construct Homo sapiens clone CCSBHm_00009157 SPG7 (SPG7) mRNA, encodes complete protein.
AB527784 - Synthetic construct DNA, clone: pF1KB5737, Homo sapiens SPG7 gene for spastic paraplegia 7, without stop codon, in Flexi system.
AF090912 - Homo sapiens clone HQ0282 PRO0282p mRNA, partial cds.
BC015411 - Homo sapiens spastic paraplegia 7 (pure and complicated autosomal recessive), mRNA (cDNA clone IMAGE:4393160), with apparent retained intron.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UQ90 (Reactome details) participates in the following event(s):

R-HSA-8949661 C2orf47:AFG3L2 binds the transit peptide of SMDT1
R-HSA-8949649 PMPCA:PMPCB cleaves the transit peptide of proSMDT1 (proEMRE)
R-HSA-8949664 Processing of SMDT1
R-HSA-8949215 Mitochondrial calcium ion transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: CAR, CMAR, NM_199367, NP_955399, PGN, Q9UQ90-2
UCSC ID: uc002fni.3
RefSeq Accession: NM_199367
Protein: Q9UQ90-2, splice isoform of Q9UQ90 CCDS: CCDS10978.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SPG7:
ataxias (Hereditary Ataxia Overview)
hsp (Hereditary Spastic Paraplegia Overview)
spg7 (Spastic Paraplegia 7)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_199367.1
exon count: 10CDS single in 3' UTR: no RNA size: 2319
ORF size: 1470CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2628.00frame shift in genome: no % Coverage: 99.27
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.