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    SPG11 SPG11 vesicle trafficking associated, spatacsin [ Homo sapiens (human) ]

    Gene ID: 80208, updated on 11-Apr-2024

    Summary

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    Official Symbol
    SPG11provided by HGNC
    Official Full Name
    SPG11 vesicle trafficking associated, spatacsinprovided by HGNC
    Primary source
    HGNC:HGNC:11226
    See related
    Ensembl:ENSG00000104133 MIM:610844; AllianceGenome:HGNC:11226
    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
    ALS5; CMT2X; KIAA1840
    Summary
    The protein encoded by this gene is a potential transmembrane protein that is phosphorylated upon DNA damage. Defects in this gene are a cause of spastic paraplegia type 11 (SPG11). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
    Expression
    Ubiquitous expression in thyroid (RPKM 18.4), testis (RPKM 13.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    15q21.1
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (44562696..44663662, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (42370662..42471634, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (44854894..44955860, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene CTD small phosphatase like 2 Neighboring gene heterogeneous nuclear ribonucleoprotein M pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:44828013-44828800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6397 Neighboring gene EIF3J divergent transcript Neighboring gene eukaryotic translation initiation factor 3 subunit J Neighboring gene ReSE screen-validated silencer GRCh37_chr15:44874604-44874775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6398 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:44879793-44880004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9341 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:44936676-44936780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9342 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:44955204-44956160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9347 Neighboring gene PAT1 homolog 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:45003536-45004198 Neighboring gene microRNA 10393 Neighboring gene beta-2-microglobulin

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Neurometabolic Dysfunction in SPG11 Hereditary Spastic Paraplegia. Regensburger M, et al. Nutrients, 2022 Nov 13. PMID 36432490, Free PMC Article
    2. "Ears of the lynx" sign and thin corpus callosum on MRI in heterozygous SPG11 mutation carriers. Rattay TW, et al. J Neurol, 2022 Nov. PMID 35614164
    3. Pattern reversal visual evoked potentials (prVEPs) in autosomal recessive hereditary spastic paraplegia with thin corpus callosum (ARHSPTCC) patients with SPG 11 mutations in Saudi Arabia, cross section hospital base study. Alfaidi N, et al. J Neurol Sci, 2022 Mar 15. PMID 35074613
    4. Hereditary spastic paraplegia type 11: Clinicogenetic lessons from 339 patients. Du J. J Clin Neurosci, 2021 Mar. PMID 33581793
    5. Hereditary spastic paraplegia type 11 (SPG11) is associated with obesity and hypothalamic damage. Cardozo-Hernández ALC, et al. J Neurol Sci, 2020 Sep 15. PMID 32593884

    See all (105) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Neurometabolic Dysfunction in SPG11 Hereditary Spastic Paraplegia.
      Title: Neurometabolic Dysfunction in SPG11 Hereditary Spastic Paraplegia.
    2. ""Ears of the lynx"" sign and thin corpus callosum on MRI in heterozygous SPG11 mutation carriers.
      Title: "Ears of the lynx" sign and thin corpus callosum on MRI in heterozygous SPG11 mutation carriers.
    3. Pattern reversal visual evoked potentials (prVEPs) in autosomal recessive hereditary spastic paraplegia with thin corpus callosum (ARHSPTCC) patients with SPG 11 mutations in Saudi Arabia, cross section hospital base study.
      Title: Pattern reversal visual evoked potentials (prVEPs) in autosomal recessive hereditary spastic paraplegia with thin corpus callosum (ARHSPTCC) patients with SPG 11 mutations in Saudi Arabia, cross section hospital base study.
    4. Transactivation response DNA-binding protein of 43 kDa proteinopathy and lysosomal abnormalities in spastic paraplegia type 11.
      Title: Transactivation response DNA-binding protein of 43 kDa proteinopathy and lysosomal abnormalities in spastic paraplegia type 11.
    5. Circ-SPG11 knockdown hampers IL-1beta-induced osteoarthritis progression via targeting miR-337-3p/ADAMTS5.
      Title: Circ-SPG11 knockdown hampers IL-1β-induced osteoarthritis progression via targeting miR-337-3p/ADAMTS5.
    6. Hereditary spastic paraplegia type 11 (SPG11) is associated with obesity and hypothalamic damage.
      Title: Hereditary spastic paraplegia type 11 (SPG11) is associated with obesity and hypothalamic damage.
    7. A novel variant in the spatacsin gene causing SPG11 in a Malian family.
      Title: A novel variant in the spatacsin gene causing SPG11 in a Malian family.
    8. Phenotypic and genotypic features of patients diagnosed with ALS in the city of Sakarya, Turkey.
      Title: Phenotypic and genotypic features of patients diagnosed with ALS in the city of Sakarya, Turkey.
    9. Description of combined ARHSP/JALS phenotype in some patients with SPG11 mutations.
      Title: Description of combined ARHSP/JALS phenotype in some patients with SPG11 mutations.
    10. Hereditary spastic paraplegia type 11: Clinicogenetic lessons from 339 patients.
      Title: Hereditary spastic paraplegia type 11: Clinicogenetic lessons from 339 patients.
    Submit: New GeneRIF Correction See all GeneRIFs (70)

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ21439, DKFZp762B1512

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within autophagosome organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in axo-dendritic transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in axo-dendritic transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chemical synaptic transmission IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chemical synaptic transmission IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cholesterol efflux IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in corticospinal tract morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in localization within membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within lysosome organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in memory IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in motor behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in motor neuron apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuromuscular junction development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phagosome-lysosome fusion involved in apoptotic cell clearance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein import into nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of store-operated calcium entry IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in skeletal muscle fiber development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synaptic vesicle transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic vesicle transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in walking behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosomal membrane HDA PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    spatacsin
    Names
    SPG11, spatacsin vesicle trafficking associated
    amyotrophic lateral sclerosis 5
    colorectal carcinoma-associated protein
    spastic paraplegia 11 (autosomal recessive)
    spastic paraplegia 11 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_008885.1 RefSeqGene

      Range
      5017..105983
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001160227.2 → NP_001153699.1  spatacsin isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      BC094704, BC150640
      Consensus CDS
      CCDS53939.1
      UniProtKB/TrEMBL
      H0YLK7
      Related
      ENSP00000445278.2, ENST00000535302.6
      Conserved Domains (1) summary
      pfam14649
      Location:1982 → 2274
      Spatacsin_C; Spatacsin C-terminus

    2. NM_001411132.1 → NP_001398061.1  spatacsin isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC009996
      Consensus CDS
      CCDS91991.1
      UniProtKB/TrEMBL
      A0A804HID9
      Related
      ENSP00000507025.1, ENST00000682065.1

    3. NM_025137.4 → NP_079413.3  spatacsin isoform 1

      See identical proteins and their annotated locations for NP_079413.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB058743, AC009996, BC094704
      Consensus CDS
      CCDS10112.1
      UniProtKB/Swiss-Prot
      A8KAX9, B9EK60, F5H3N6, Q4VC11, Q58G86, Q69YG6, Q6NW01, Q8N270, Q8TBU9, Q96JI7, Q9H734
      UniProtKB/TrEMBL
      C4B7M4
      Related
      ENSP00000261866.7, ENST00000261866.12
      Conserved Domains (1) summary
      pfam14649
      Location:2095 → 2387
      Spatacsin_C; Spatacsin C-terminus

    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
      44562696..44663662 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433144.1 → XP_047289100.1  spatacsin isoform X1

    2. XM_047433146.1 → XP_047289102.1  spatacsin isoform X5

    3. XM_006720701.4 → XP_006720764.1  spatacsin isoform X3

      UniProtKB/TrEMBL
      A0A804HKV6
      Related
      ENSP00000508089.1, ENST00000682788.1

    4. XM_017022635.3 → XP_016878124.1  spatacsin isoform X2

      UniProtKB/TrEMBL
      A0A804HKV6

    5. XM_047433145.1 → XP_047289101.1  spatacsin isoform X4

      Related
      ENSP00000507557.1, ENST00000683121.1

    RNA

    1. XR_001751402.2 RNA Sequence

      Related
      ENST00000682915.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      42370662..42471634 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378921.1 → XP_054234896.1  spatacsin isoform X1

    2. XM_054378925.1 → XP_054234900.1  spatacsin isoform X5

    3. XM_054378923.1 → XP_054234898.1  spatacsin isoform X3

    4. XM_054378922.1 → XP_054234897.1  spatacsin isoform X2

    5. XM_054378924.1 → XP_054234899.1  spatacsin isoform X4

    RNA

    1. XR_008489013.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96JI7.3 GenPept UniProtKB/Swiss-Prot:Q96JI7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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