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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
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Genomic context

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See SPG11 in Genome Data Viewer
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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