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Aliases for SPTBN2 Gene

Aliases for SPTBN2 Gene

  • Spectrin Beta, Non-Erythrocytic 2 2 3 5
  • Spinocerebellar Ataxia 5 Protein 3 4
  • Beta-III Spectrin 3 4
  • SCA5 3 4
  • Glutamate Transporter EAAT4-Associated Protein 41 3
  • Spectrin Beta Chain, Non-Erythrocytic 2 3
  • Spectrin, Non-Erythroid Beta Chain 2 3
  • Spectrin Beta Chain, Brain 2 3
  • Spectrin Beta III Sigma 2 3
  • Spinocerebellar Ataxia 5 2
  • KIAA0302 4
  • GTRAP41 3
  • SCAR14 3

External Ids for SPTBN2 Gene

Previous HGNC Symbols for SPTBN2 Gene

  • SCA5

Previous GeneCards Identifiers for SPTBN2 Gene

  • GC11M068986
  • GC11M068134
  • GC11M066228
  • GC11M066209
  • GC11M066453
  • GC11M062780

Summaries for SPTBN2 Gene

Entrez Gene Summary for SPTBN2 Gene

  • Spectrins are principle components of a cell's membrane-cytoskeleton and are composed of two alpha and two beta spectrin subunits. The protein encoded by this gene (SPTBN2), is called spectrin beta non-erythrocytic 2 or beta-III spectrin. It is related to, but distinct from, the beta-II spectrin gene which is also known as spectrin beta non-erythrocytic 1 (SPTBN1). SPTBN2 regulates the glutamate signaling pathway by stabilizing the glutamate transporter EAAT4 at the surface of the plasma membrane. Mutations in this gene cause a form of spinocerebellar ataxia, SCA5, that is characterized by neurodegeneration, progressive locomotor incoordination, dysarthria, and uncoordinated eye movements. [provided by RefSeq, Dec 2009]

GeneCards Summary for SPTBN2 Gene

SPTBN2 (Spectrin Beta, Non-Erythrocytic 2) is a Protein Coding gene. Diseases associated with SPTBN2 include Spinocerebellar Ataxia 5 and Spinocerebellar Ataxia, Autosomal Recessive 14. Among its related pathways are RET signaling and Transport to the Golgi and subsequent modification. Gene Ontology (GO) annotations related to this gene include actin binding and phospholipid binding. An important paralog of this gene is SPTBN1.

UniProtKB/Swiss-Prot for SPTBN2 Gene

  • Probably plays an important role in neuronal membrane skeleton.

Gene Wiki entry for SPTBN2 Gene

Additional gene information for SPTBN2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SPTBN2 Gene

Genomics for SPTBN2 Gene

GeneHancer (GH) Regulatory Elements for SPTBN2 Gene

Promoters and enhancers for SPTBN2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J066743 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 652.9 -15.5 -15471 2.9 ARID4B SIN3A ZBTB7B YY1 POLR2B ZNF207 ZNF143 FOS SP3 SP5 SPTBN2 GC11M066742 C11orf80 EIF1AD ENSG00000258297 RBM14 KDM2A RBM4 MRPL11 SART1
GH11J066727 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE 655.5 +1.3 1282 1.3 HDGF SIN3A ZNF2 ZNF48 YY1 ZNF766 GLIS2 ELK1 ZNF263 RXRA SPTBN2 ENSG00000258297 RBM14 PC SF3B2 RBM4 SART1 MUS81 RCE1 ENSG00000255038
GH11J066728 Enhancer 0.9 ENCODE 650.7 +0.2 233 0.8 HDAC1 HDGF PKNOX1 ATF1 ARNT NFRKB ZBTB40 ZNF335 TCF12 GLIS2 SPTBN2 GC11M066719 GC11M066718
GH11J066676 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 11.4 +51.4 51416 2.8 HDGF PKNOX1 CLOCK SMAD1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 RBM4B GC11P066677 RN7SL12P SPTBN2 C11orf80 LRFN4 PC ZDHHC24 ACTN3 RBM14-RBM4
GH11J066694 Enhancer 1.2 Ensembl ENCODE 12.1 +34.4 34387 1 HDGF ARNT ARID4B SIN3A ZNF2 IRF4 YY1 SLC30A9 E2F8 ZNF143 RCE1 ENSG00000258297 RBM14 SF3B2 RBM4 SART1 MUS81 KAT5 ENSG00000255038 RAD9A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPTBN2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SPTBN2 gene promoter:
  • Sox9
  • LCR-F1
  • Spz1
  • Arnt
  • C/EBPbeta
  • Nkx2-2
  • Roaz
  • AP-4
  • GR
  • AML1a

Genomic Locations for SPTBN2 Gene

Genomic Locations for SPTBN2 Gene
chr11:66,682,496-66,729,237
(GRCh38/hg38)
Size:
46,742 bases
Orientation:
Minus strand
chr11:66,452,719-66,496,697
(GRCh37/hg19)
Size:
43,979 bases
Orientation:
Minus strand

Genomic View for SPTBN2 Gene

Genes around SPTBN2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPTBN2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPTBN2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPTBN2 Gene

Proteins for SPTBN2 Gene

  • Protein details for SPTBN2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15020-SPTN2_HUMAN
    Recommended name:
    Spectrin beta chain, non-erythrocytic 2
    Protein Accession:
    O15020
    Secondary Accessions:
    • O14872
    • O14873

    Protein attributes for SPTBN2 Gene

    Size:
    2390 amino acids
    Molecular mass:
    271325 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA32700.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SPTBN2 Gene

    Alternative splice isoforms for SPTBN2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPTBN2 Gene

Post-translational modifications for SPTBN2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SPTBN2 Gene

Domains & Families for SPTBN2 Gene

Gene Families for SPTBN2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for SPTBN2 Gene

Graphical View of Domain Structure for InterPro Entry

O15020

UniProtKB/Swiss-Prot:

SPTN2_HUMAN :
  • Belongs to the spectrin family.
Family:
  • Belongs to the spectrin family.
genes like me logo Genes that share domains with SPTBN2: view

Function for SPTBN2 Gene

Molecular function for SPTBN2 Gene

UniProtKB/Swiss-Prot Function:
Probably plays an important role in neuronal membrane skeleton.

Phenotypes From GWAS Catalog for SPTBN2 Gene

Gene Ontology (GO) - Molecular Function for SPTBN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA --
GO:0005088 Ras guanyl-nucleotide exchange factor activity TAS --
GO:0005200 structural constituent of cytoskeleton TAS 9826670
GO:0005515 protein binding IEA --
GO:0005543 phospholipid binding IEA --
genes like me logo Genes that share ontologies with SPTBN2: view
genes like me logo Genes that share phenotypes with SPTBN2: view

Human Phenotype Ontology for SPTBN2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SPTBN2 Gene

MGI Knock Outs for SPTBN2:
  • Sptbn2 Sptbn2<tm1b(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTBN2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SPTBN2 Gene

Localization for SPTBN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPTBN2 Gene

Cytoplasm, cytoskeleton. Cytoplasm, cell cortex.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPTBN2 gene
Compartment Confidence
extracellular 5
cytoskeleton 5
cytosol 5
plasma membrane 3
nucleus 2
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (3)
  • Cytosol (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPTBN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space HDA 22664934
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA,TAS --
GO:0005856 cytoskeleton IEA --
GO:0005938 cell cortex IEA --
genes like me logo Genes that share ontologies with SPTBN2: view

Pathways & Interactions for SPTBN2 Gene

SuperPathways for SPTBN2 Gene

SuperPathway Contained pathways
1 RET signaling
2 Transport to the Golgi and subsequent modification
3 Sertoli-Sertoli Cell Junction Dynamics
4 Developmental Biology
5 Cytokine Signaling in Immune system
genes like me logo Genes that share pathways with SPTBN2: view

Gene Ontology (GO) - Biological Process for SPTBN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000165 MAPK cascade TAS --
GO:0006888 ER to Golgi vesicle-mediated transport TAS --
GO:0007010 cytoskeleton organization IEA --
GO:0007411 axon guidance TAS --
GO:0007416 synapse assembly IEA --
genes like me logo Genes that share ontologies with SPTBN2: view

No data available for SIGNOR curated interactions for SPTBN2 Gene

Drugs & Compounds for SPTBN2 Gene

No Compound Related Data Available

Transcripts for SPTBN2 Gene

Unigene Clusters for SPTBN2 Gene

Spectrin, beta, non-erythrocytic 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTBN2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SPTBN2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21a ·
SP1:
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:
SP10:
SP11:
SP12:

ExUns: 21b ^ 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30a · 30b ^ 31a · 31b
SP1: -
SP2:
SP3:
SP4:
SP5: -
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for SPTBN2 Gene

GeneLoc Exon Structure for
SPTBN2
ECgene alternative splicing isoforms for
SPTBN2

Expression for SPTBN2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SPTBN2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SPTBN2 Gene

This gene is overexpressed in Brain - Cerebellum (x4.3) and Brain - Cortex (x4.1).

Protein differential expression in normal tissues from HIPED for SPTBN2 Gene

This gene is overexpressed in Frontal cortex (18.9), Salivary gland (9.7), Retina (6.2), and Cervix (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SPTBN2 Gene



NURSA nuclear receptor signaling pathways regulating expression of SPTBN2 Gene:

SPTBN2

SOURCE GeneReport for Unigene cluster for SPTBN2 Gene:

Hs.26915

mRNA Expression by UniProt/SwissProt for SPTBN2 Gene:

O15020-SPTN2_HUMAN
Tissue specificity: Highly expressed in brain, kidney, pancreas, and liver, and at lower levels in lung and placenta.

Evidence on tissue expression from TISSUES for SPTBN2 Gene

  • Heart(5)
  • Liver(4.9)
  • Nervous system(4.7)
  • Adrenal gland(4)
  • Lung(3.7)
  • Blood(3.6)
  • Kidney(3.6)
  • Gall bladder(3.3)
  • Pancreas(3.3)
  • Eye(2.7)
  • Intestine(2.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SPTBN2 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • face
  • head
Limb:
  • lower limb
  • upper limb
General:
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with SPTBN2: view

No data available for Protein tissue co-expression partners for SPTBN2 Gene

Orthologs for SPTBN2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SPTBN2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SPTBN2 34 33
  • 99.25 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SPTBN2 34
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SPTBN2 34 33
  • 90.1 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SPTBN2 34
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sptbn2 16 34 33
  • 87.59 (n)
rat
(Rattus norvegicus)
Mammalia Sptbn2 33
  • 87.52 (n)
oppossum
(Monodelphis domestica)
Mammalia SPTBN2 34
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves SPTBN2 34
  • 68 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SPTBN2 34
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486199 33
  • 65.31 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC558044 33
  • 66.77 (n)
sptbn2 34
  • 66 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta &bgr;-Spec 35
  • 51 (a)
beta-Spec 34
  • 49 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea unc-70 34 35
  • 46 (a)
OneToMany
M116.5 35
  • 41 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 48 (a)
OneToMany
Species where no ortholog for SPTBN2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SPTBN2 Gene

ENSEMBL:
Gene Tree for SPTBN2 (if available)
TreeFam:
Gene Tree for SPTBN2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPTBN2: view image

Paralogs for SPTBN2 Gene

Paralogs for SPTBN2 Gene

(18) SIMAP similar genes for SPTBN2 Gene using alignment to 5 proteins:

  • SPTN2_HUMAN
  • A4QPE4_HUMAN
  • C1KC08_HUMAN
  • E9PJZ2_HUMAN
  • Q45KQ1_HUMAN
genes like me logo Genes that share paralogs with SPTBN2: view

Variants for SPTBN2 Gene

Sequence variations from dbSNP and Humsavar for SPTBN2 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs11227572 likely-benign, Spinocerebellar Ataxia, Dominant 66,692,959(-) G/A/C genic_downstream_transcript_variant, intron_variant
rs114241603 benign, likely-benign, not specified, Spinocerebellar Ataxia, Dominant 66,700,817(-) C/T coding_sequence_variant, synonymous_variant
rs114331192 likely-benign, Spinocerebellar Ataxia, Dominant 66,710,912(-) A/G intron_variant
rs114788199 likely-benign, benign, Spinocerebellar Ataxia, Dominant, Spinocerebellar ataxia 5 66,699,496(-) T/C coding_sequence_variant, missense_variant
rs115062978 likely-benign, Spinocerebellar Ataxia, Dominant 66,694,195(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for SPTBN2 Gene

Variant ID Type Subtype PubMed ID
nsv468602 CNV loss 19166990
nsv518919 CNV loss 19592680
nsv522277 CNV loss 19592680
nsv555225 CNV loss 21841781

Variation tolerance for SPTBN2 Gene

Residual Variation Intolerance Score: 0.518% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.21; 69.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPTBN2 Gene

Human Gene Mutation Database (HGMD)
SPTBN2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPTBN2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPTBN2 Gene

Disorders for SPTBN2 Gene

MalaCards: The human disease database

(14) MalaCards diseases for SPTBN2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

UniProtKB/Swiss-Prot

SPTN2_HUMAN
  • Spinocerebellar ataxia 5 (SCA5) [MIM:600224]: Spinocerebellar ataxia is a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA5 is an autosomal dominant cerebellar ataxia (ADCA). It is a slowly progressive disorder with variable age at onset, ranging between 10 and 50 years. {ECO:0000269 PubMed:16429157, ECO:0000269 PubMed:22914369}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Spinocerebellar ataxia, autosomal recessive, 14 (SCAR14) [MIM:615386]: Spinocerebellar ataxia is a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAR14 is characterized by delayed psychomotor development, severe early onset gait ataxia, eye movement abnormalities, cerebellar atrophy on brain imaging, and intellectual disability. {ECO:0000269 PubMed:23236289, ECO:0000269 PubMed:23838597}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SPTBN2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SPTBN2: view

No data available for Genatlas for SPTBN2 Gene

Publications for SPTBN2 Gene

  1. Spectrin mutations cause spinocerebellar ataxia type 5. (PMID: 16429157) Ikeda Y … Ranum LP (Nature genetics 2006) 2 3 4 22 58
  2. A widely expressed betaIII spectrin associated with Golgi and cytoplasmic vesicles. (PMID: 9826670) Stankewich MC … Lux SE (Proceedings of the National Academy of Sciences of the United States of America 1998) 2 3 4 22 58
  3. Screening of the SPTBN2 (SCA5) gene in German SCA patients. (PMID: 17940722) Zühlke C … Bürk K (Journal of neurology 2007) 3 22 44 58
  4. Autosomal dominant SCA5 and autosomal recessive infantile SCA are allelic conditions resulting from SPTBN2 mutations. (PMID: 23838597) Elsayed SM … Bolz HJ (European journal of human genetics : EJHG 2014) 3 4 58
  5. Recessive mutations in SPTBN2 implicate β-III spectrin in both cognitive and motor development. (PMID: 23236289) Lise S … Németh AH (PLoS genetics 2012) 3 4 58

Products for SPTBN2 Gene

Sources for SPTBN2 Gene

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