Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. This gene is one member of a family of beta-spectrin genes. The ... See more...

Aliases for SPTBN4 Gene

Aliases for SPTBN4 Gene

  • Spectrin Beta, Non-Erythrocytic 4 2 3 5
  • SPTBN3 2 3 4
  • Spectrin Beta Chain, Non-Erythrocytic 4 3 4
  • Spectrin, Non-Erythroid Beta Chain 3 3 4
  • Beta-IV Spectrin 3 4
  • KIAA1642 2 4
  • Spectrin Beta Chain, Brain 3 3
  • NEDHND 3
  • SPTBN4 5
  • SPNB4 3
  • CMND 3
  • QV 3

External Ids for SPTBN4 Gene

Previous GeneCards Identifiers for SPTBN4 Gene

  • GC19P041612
  • GC19P041364
  • GC19P045649
  • GC19P045664
  • GC19P045663
  • GC19P040973
  • GC19P037385

Summaries for SPTBN4 Gene

Entrez Gene Summary for SPTBN4 Gene

  • Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. This gene is one member of a family of beta-spectrin genes. The encoded protein localizes to the nuclear matrix, PML nuclear bodies, and cytoplasmic vesicles. A highly similar gene in the mouse is required for localization of specific membrane proteins in polarized regions of neurons. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for SPTBN4 Gene

SPTBN4 (Spectrin Beta, Non-Erythrocytic 4) is a Protein Coding gene. Diseases associated with SPTBN4 include Neurodevelopmental Disorder With Hypotonia, Neuropathy, And Deafness and Spinocerebellar Ataxia 5. Among its related pathways are RET signaling and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include actin binding and phospholipid binding. An important paralog of this gene is SPTBN1.

Gene Wiki entry for SPTBN4 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPTBN4 Gene

Genomics for SPTBN4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SPTBN4 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPTBN4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPTBN4

Top Transcription factor binding sites by QIAGEN in the SPTBN4 gene promoter:
  • Bach1
  • c-Ets-1
  • Ik-2
  • MyoD
  • N-Myc
  • NF-1
  • NF-1/L
  • Pax-4a
  • SEF-1 (1)
  • XBP-1

Genomic Locations for SPTBN4 Gene

Genomic Locations for SPTBN4 Gene
chr19:40,466,241-40,576,464
(GRCh38/hg38)
Size:
110,224 bases
Orientation:
Plus strand
chr19:40,972,148-41,082,370
(GRCh37/hg19)
Size:
110,223 bases
Orientation:
Plus strand

Genomic View for SPTBN4 Gene

Genes around SPTBN4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPTBN4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPTBN4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPTBN4 Gene

Proteins for SPTBN4 Gene

  • Protein details for SPTBN4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H254-SPTN4_HUMAN
    Recommended name:
    Spectrin beta chain, non-erythrocytic 4
    Protein Accession:
    Q9H254
    Secondary Accessions:
    • E9PGQ5
    • Q9H1K7
    • Q9H1K8
    • Q9H1K9
    • Q9H253
    • Q9H3G8
    • Q9HCD0

    Protein attributes for SPTBN4 Gene

    Size:
    2564 amino acids
    Molecular mass:
    288985 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SPTBN4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPTBN4 Gene

Post-translational modifications for SPTBN4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SPTBN4 Gene

Domains & Families for SPTBN4 Gene

Gene Families for SPTBN4 Gene

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

Protein Domains for SPTBN4 Gene

InterPro:
Blocks:
  • Pleckstrin-like
  • Actin-binding, actinin-type
  • Calponin-like actin-binding
  • Spectrin repeat
  • Spectrin pleckstrin homology domain signature
ProtoNet:

Suggested Antigen Peptide Sequences for SPTBN4 Gene

GenScript: Design optimal peptide antigens:
  • Spectrin beta IV (Q9H253_HUMAN)
  • Spectrin, non-erythroid beta chain 3 (SPTN4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H254

UniProtKB/Swiss-Prot:

SPTN4_HUMAN :
  • Belongs to the spectrin family.
Family:
  • Belongs to the spectrin family.
genes like me logo Genes that share domains with SPTBN4: view

Function for SPTBN4 Gene

Phenotypes From GWAS Catalog for SPTBN4 Gene

Gene Ontology (GO) - Molecular Function for SPTBN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA,ISS --
GO:0005200 structural constituent of cytoskeleton IEA,TAS 11294830
GO:0005515 protein binding IEA,IPI 11086001
GO:0005543 phospholipid binding IEA --
GO:0019902 phosphatase binding IPI 11086001
genes like me logo Genes that share ontologies with SPTBN4: view
genes like me logo Genes that share phenotypes with SPTBN4: view

Human Phenotype Ontology for SPTBN4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SPTBN4 Gene

MGI Knock Outs for SPTBN4:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTBN4

No data available for Molecular function , Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for SPTBN4 Gene

Localization for SPTBN4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPTBN4 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 SPTBN4 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 5
plasma membrane 4
extracellular 4
mitochondrion 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPTBN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005737 cytoplasm IEA,IDA 11294830
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
GO:0005884 actin filament ISS --
genes like me logo Genes that share ontologies with SPTBN4: view

Pathways & Interactions for SPTBN4 Gene

PathCards logo

SuperPathways for SPTBN4 Gene

SuperPathway Contained pathways
1 RET signaling
2 Transport to the Golgi and subsequent modification
3 Sertoli-Sertoli Cell Junction Dynamics
.38
.36
4 Developmental Biology
5 Cytokine Signaling in Immune system
genes like me logo Genes that share pathways with SPTBN4: view

Pathways by source for SPTBN4 Gene

2 Qiagen pathways for SPTBN4 Gene
  • Epithelial Tight Junctions
  • Sertoli-Sertoli Cell Junction Dynamics

Gene Ontology (GO) - Biological Process for SPTBN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000165 MAPK cascade TAS --
GO:0002028 regulation of sodium ion transport ISS --
GO:0006888 ER to Golgi vesicle-mediated transport TAS --
GO:0007010 cytoskeleton organization IEA --
GO:0007016 cytoskeletal anchoring at plasma membrane TAS --
genes like me logo Genes that share ontologies with SPTBN4: view

No data available for SIGNOR curated interactions for SPTBN4 Gene

Drugs & Compounds for SPTBN4 Gene

(1) Additional Compounds for SPTBN4 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SPTBN4: view

Transcripts for SPTBN4 Gene

mRNA/cDNA for SPTBN4 Gene

2 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTBN4

Alternative Splicing Database (ASD) splice patterns (SP) for SPTBN4 Gene

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

ExUns: 20c ^ 21 ^ 22a · 22b ^ 23 ^ 24a · 24b ^ 25a · 25b ^ 26a · 26b ^ 27a · 27b · 27c
SP1:
SP2:
SP3: -
SP4:
SP5: - -
SP6: -
SP7:
SP8:
SP9:
SP10: -
SP11:

Relevant External Links for SPTBN4 Gene

GeneLoc Exon Structure for
SPTBN4

Expression for SPTBN4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPTBN4 Gene

mRNA differential expression in normal tissues according to GTEx for SPTBN4 Gene

This gene is overexpressed in Brain - Cerebellum (x7.6), Brain - Cerebellar Hemisphere (x7.5), Brain - Cortex (x4.7), and Brain - Frontal Cortex (BA9) (x4.1).

Protein differential expression in normal tissues from HIPED for SPTBN4 Gene

This gene is overexpressed in Frontal cortex (23.4), Lung (8.6), and Bone marrow stromal cell (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SPTBN4 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPTBN4

SOURCE GeneReport for Unigene cluster for SPTBN4 Gene:

Hs.32706

mRNA Expression by UniProt/SwissProt for SPTBN4 Gene:

Q9H254-SPTN4_HUMAN
Tissue specificity: Expressed in skeletal muscle at the sarcolemma and in the muscle capillaries (at protein level) (PubMed:28540413). Abundantly expressed in brain and pancreatic islets (PubMed:11086001).

Evidence on tissue expression from TISSUES for SPTBN4 Gene

  • Heart(5)
  • Liver(4.9)
  • Nervous system(4.8)
  • Eye(4.3)
  • Kidney(3.7)
  • Adrenal gland(3.6)
  • Blood(3.5)
  • Gall bladder(2.4)
  • Intestine(2)
genes like me logo Genes that share expression patterns with SPTBN4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPTBN4 Gene

Orthologs for SPTBN4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SPTBN4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SPTBN4 31
  • 100 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SPTBN4 30 31
  • 92.32 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SPTBN4 30 31
  • 91.97 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sptbn4 30
  • 88.6 (n)
Mouse
(Mus musculus)
Mammalia Sptbn4 30 17 31
  • 88.56 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SPTBN4 31
  • 82 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SPTBN4 31
  • 69 (a)
OneToOne
Chicken
(Gallus gallus)
Aves -- 31
  • 39 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia SPTBN4 31
  • 66 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sptbn4 30
  • 64.69 (n)
Zebrafish
(Danio rerio)
Actinopterygii SPTBN4 (3 of 3) 31
  • 63 (a)
OneToMany
SPTBN4 (2 of 3) 31
  • 54 (a)
OneToMany
SPTBN4 (1 of 3) 31
  • 40 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta beta-Spec 31
  • 43 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea M116.5 32
  • 43 (a)
unc-70 31
  • 40 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 42 (a)
OneToMany
Species where no ortholog for SPTBN4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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 SPTBN4 Gene

ENSEMBL:
Gene Tree for SPTBN4 (if available)
TreeFam:
Gene Tree for SPTBN4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPTBN4: view image

Paralogs for SPTBN4 Gene

(16) SIMAP similar genes for SPTBN4 Gene using alignment to 5 proteins:

  • SPTN4_HUMAN
  • C9JRP8_HUMAN
  • C9JY79_HUMAN
  • M0QZQ3_HUMAN
  • M0R1V6_HUMAN
genes like me logo Genes that share paralogs with SPTBN4: view

Variants for SPTBN4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPTBN4 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
694501 Uncertain Significance: Muscular hypotonia; Global developmental delay; Delayed myelination 40,532,624(+) G/A SPLICE_ACCEPTOR_VARIANT
714786 Benign: not provided 40,513,004(+) G/A MISSENSE_VARIANT
714787 Benign: not provided 40,515,398(+) C/T SYNONYMOUS_VARIANT
716479 Benign: not provided 40,572,136(+) G/C MISSENSE_VARIANT
722234 Likely Benign: not provided 40,512,982(+) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for SPTBN4 Gene

Structural Variations from Database of Genomic Variants (DGV) for SPTBN4 Gene

Variant ID Type Subtype PubMed ID
esv1007999 CNV deletion 20482838
esv2667159 CNV deletion 23128226
esv2676684 CNV deletion 23128226
esv2718565 CNV deletion 23290073
esv3644351 CNV loss 21293372
esv3644352 CNV loss 21293372
esv3644353 CNV loss 21293372
esv3644355 CNV loss 21293372
esv3644356 CNV loss 21293372
esv992020 CNV loss 20482838
nsv138059 CNV insertion 16902084
nsv477924 CNV novel sequence insertion 20440878
nsv478209 CNV novel sequence insertion 20440878

Variation tolerance for SPTBN4 Gene

Residual Variation Intolerance Score: 21.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.65; 96.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPTBN4 Gene

Human Gene Mutation Database (HGMD)
SPTBN4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPTBN4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPTBN4 Gene

Disorders for SPTBN4 Gene

MalaCards: The human disease database

(11) MalaCards diseases for SPTBN4 Gene - From: OMIM, ClinVar, GTR, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SPTN4_HUMAN
  • Neurodevelopmental disorder with hypotonia, neuropathy, and deafness (NEDHND) [MIM:617519]: An autosomal recessive disorder characterized by congenital myopathy with hypotonia and muscle weakness manifesting after birth and progressing to generalized muscle atrophy, central deafness with absent brainstem-evoked potentials, and a combined axonal and demyelinating motor neuropathy. {ECO:0000269 PubMed:28540413}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SPTBN4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SPTBN4: view

No data available for Genatlas for SPTBN4 Gene

Publications for SPTBN4 Gene

  1. betaIV spectrin, a new spectrin localized at axon initial segments and nodes of ranvier in the central and peripheral nervous system. (PMID: 11086001) Berghs S … Solimena M (The Journal of cell biology 2000) 2 3 4 23
  2. A new spectrin, beta IV, has a major truncated isoform that associates with promyelocytic leukemia protein nuclear bodies and the nuclear matrix. (PMID: 11294830) Tse WT … Lux SE (The Journal of biological chemistry 2001) 3 4 23
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  4. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T … Yamada Y (International journal of molecular medicine 2010) 3 41
  5. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M … Yamada Y (American journal of hypertension 2010) 3 41

Products for SPTBN4 Gene