SPTBN2

gene
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Summary

SPTBN2 (spectrin beta, non-erythrocytic 2, HGNC:11276) is a protein-coding gene on chromosome 11q13.2, encoding Spectrin beta chain, non-erythrocytic 2 (O15020). Probably plays an important role in neuronal membrane skeleton.

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.

Source: NCBI Gene 6712 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): autosomal recessive spinocerebellar ataxia 14 (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 6
  • Clinical variants (ClinVar): 1,407 total — 25 pathogenic, 28 likely-pathogenic
  • Phenotypes (HPO): 45
  • MANE Select transcript: NM_006946

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11276
Approved symbolSPTBN2
Namespectrin beta, non-erythrocytic 2
Location11q13.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000173898
Ensembl biotypeprotein_coding
OMIM604985
Entrez6712

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 14 protein_coding, 5 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000309996, ENST00000528051, ENST00000529997, ENST00000530665, ENST00000530775, ENST00000532650, ENST00000532902, ENST00000533211, ENST00000611817, ENST00000617502, ENST00000647510, ENST00000682471, ENST00000713737, ENST00000713738, ENST00000713739, ENST00000713740, ENST00000713741, ENST00000713742, ENST00000888769, ENST00000930530, ENST00000930531, ENST00000961397

RefSeq mRNA: 2 — MANE Select: NM_006946 NM_001411025, NM_006946

CCDS: CCDS8150, CCDS91511

Canonical transcript exons

ENST00000533211 — 38 exons

ExonStartEnd
ENSE000011879016668865366688849
ENSE000011879276669003966690283
ENSE000011879356669128466691658
ENSE000011879406669253666692740
ENSE000011879506669297066693100
ENSE000011879566669318666693446
ENSE000011879656669377266693861
ENSE000011879796669413966694363
ENSE000011880096669899266699082
ENSE000011880176669940666699608
ENSE000011880266670052666701282
ENSE000011880336670158466701721
ENSE000011880406670459866705468
ENSE000011880496670568466705837
ENSE000011880536670751666707818
ENSE000011880656670814166708299
ENSE000011880716670890266709019
ENSE000011880806671058266710769
ENSE000011880966671363166713746
ENSE000011881106671409166714171
ENSE000011881386671583066715981
ENSE000021402456672874166729216
ENSE000021881376668249766686104
ENSE000024300516671091766711029
ENSE000024525866669863966698785
ENSE000024858506671431666714407
ENSE000025154556671522266715395
ENSE000036222246668980566689943
ENSE000036509896669627766696540
ENSE000036632486668909666689180
ENSE000040210926668816966688311
ENSE000040210946672135066721440
ENSE000040210956668742766687647
ENSE000040210996672108466721262
ENSE000040211006668639866686440
ENSE000040211016668699466687167
ENSE000040211026668786866687918
ENSE000040211036668800466688079

Expression profiles

Bgee: expression breadth ubiquitous, 238 present calls, max score 99.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.3978 / max 387.5476, expressed in 1014 samples.

FANTOM5 promoters (18 alternative TSS)

Promoter IDTPM avgSamples expressed
1208382.3522768
1208332.1650286
1208462.0404177
1208400.6495319
1208470.594891
1208320.4207153
1208370.4138234
1208430.3550123
1208440.2821134
1208390.2649114

Top tissues by expression

293 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489099.10gold quality
cerebellar hemisphereUBERON:000224598.75gold quality
cerebellar cortexUBERON:000212998.67gold quality
right frontal lobeUBERON:000281098.32gold quality
skin of legUBERON:000151198.05gold quality
skin of abdomenUBERON:000141697.84gold quality
cortical plateUBERON:000534397.68gold quality
cerebellumUBERON:000203797.52gold quality
ganglionic eminenceUBERON:000402396.90gold quality
prefrontal cortexUBERON:000045196.76gold quality
zone of skinUBERON:000001496.74gold quality
left testisUBERON:000453396.73gold quality
right testisUBERON:000453496.73gold quality
metanephros cortexUBERON:001053396.58gold quality
cingulate cortexUBERON:000302796.30gold quality
anterior cingulate cortexUBERON:000983596.28gold quality
lower esophagus mucosaUBERON:003583496.18gold quality
nucleus accumbensUBERON:000188295.99gold quality
esophagus mucosaUBERON:000246995.57gold quality
amygdalaUBERON:000187695.32gold quality
Brodmann (1909) area 9UBERON:001354095.12gold quality
gingivaUBERON:000182894.86gold quality
gingival epitheliumUBERON:000194994.68gold quality
upper leg skinUBERON:000426294.59gold quality
dorsolateral prefrontal cortexUBERON:000983494.43gold quality
frontal cortexUBERON:000187094.35gold quality
neocortexUBERON:000195094.31gold quality
oral cavityUBERON:000016794.11gold quality
mammalian vulvaUBERON:000099793.90gold quality
skin of hipUBERON:000155493.61gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.98
E-MTAB-6142no18.04

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting SPTBN2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6133100.0066.482064
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-4692100.0067.322066
HSA-MIR-451499.9967.101870
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-497-5P99.9271.832674
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-424-5P99.8971.902641
HSA-MIR-6838-5P99.8971.942690
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-221-5P99.8665.451052
HSA-MIR-807399.8665.211118
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-149-3P99.7268.223963
HSA-MIR-548AU-3P99.7068.221373
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-64699.6867.841645
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-4690-5P99.6566.24813
HSA-MIR-182799.6368.573265

Literature-anchored findings (GeneRIF, showing 31)

  • beta-III spectrin (SPTBN2) mutations cause spinocerebellar ataxia type 5 (SCA5) in an 11-generation American kindred descended from President Lincoln’s grandparents and two additional families. (PMID:16429157)
  • None of the Spinocerebellar Ataxia individuals tested had evidence for one of the known SCA5 mutations. (PMID:17940722)
  • Adducin acting through spectrin provides a novel mechanism to regulate global properties of the lateral membrane of bronchial epithelial cells. (PMID:18003973)
  • the crystal structure of the ankyrin-binding domain of human beta2-spectrin at 1.95 A resolution together with mutagenesis data identifying the binding surface for ankyrins on beta2-spectrin. (PMID:19098307)
  • TGF-beta signaling, particularly beta2SP, plays a critical role in hepatocyte proliferation and transitional phenotype. (PMID:20131405)
  • A mouse model lacking full-length beta-III spectrin reproduces features of human spinocerebellar ataxia type 5 including gait abnormalities, tremor, deteriorating motor coordination, Purkinje cell loss, and cerebellar atrophy. (PMID:20371805)
  • Results suggest that it is possible for cellular proteins to differentially associate with the C-termini of different beta-spectrin isoforms to regulate alpha- and beta-spectrin association to form functional spectrin tetramers. (PMID:21412925)
  • This review summarizes data showing that beta-III spectrin mutations are a novel cause of neurodegenerative disease, which may affect the stabilization or trafficking of membrane proteins. (PMID:21827906)
  • two gene markers (CNKSR3 and SPTBN2) differentiate between aspirin-exacerbated respiratory disease and aspirin-tolerant asthma with a perfect discriminative power (PMID:22457146)
  • A novel missense mutation within a SPTBN2 spectrin repeat encoded by exon 12 was found in a family with spinocerebellar ataxia type 5. (PMID:22843192)
  • betaIII spectrin regulates the structural integrity and the secretory protein transport of the Golgi complex (PMID:23233669)
  • the identification of SPARCA1 and normal heterozygous carriers of the stop codon in SPTBN2 provides insights into the mechanism of molecular dominance in SCA5 and demonstrates that the cell-specific repertoire of spectrin subunits (PMID:23236289)
  • A homozygous SPTBN2 nonsense mutation underlying infantile ataxia and psychomotor delay in a human family. (PMID:23838597)
  • Mutant beta-III spectrin causes mislocalization and dysfunction of mGluR1alpha at dendritic spines. (PMID:25057192)
  • First Japanese spinocerebellar ataxia type 5 (SCA5) family with a novel heterozygous three-nucleotide in-frame deletion mutation in the SPTBN2 gene. (PMID:25142508)
  • investigated using either targeted next generation sequencing or trio-based exome sequencing and were found to have mutations in three different genes, KCNC3, ITPR1 and SPTBN2 (PMID:25981959)
  • TGF-beta/beta2-spectrin/CTCF-regulated tumor suppression in human stem cell disorder Beckwith-Wiedemann syndrome. (PMID:26784546)
  • This study indicates that high-affinity actin binding of L253P beta-III-spectrin is a likely driver of neurodegeneration. (PMID:26883385)
  • beta2-Spectrin, a TGF-beta mediator and signaling molecule, is cleaved and activated by caspase-3/7, consequently enhancing apoptosis and transcriptional control to determine cell fate upon liver damage. (PMID:26884715)
  • Cardiac beta2-spectrin and downstream molecules are regulated in multiple forms of cardiovascular disease via Ca(2+)- and calpain-dependent proteolysis. (PMID:27106045)
  • the proposed methodology is validated against betaII-spectrin protein, a brain injury validated biomarker (PMID:28112201)
  • SCA5 missense mutation found in the spinocerebellar ataxia type 5 perturbs a closed-open structural equilibrium in the SCA5-actin-binding domain by lowering the energetic barrier between structural states. (PMID:29116080)
  • Study reviews the previously reported SPTBN2 mutations and cases. Moreover, the novel homozygous missense variant (c.1572C>T; p.R414C) in two brothers adds up to the literature for the infantile-onset form of autosomal recessive ataxia associated with SPTBN2. (PMID:29196973)
  • High SPTBN2 expression is associated with malignant peripheral nerve sheath tumors. (PMID:29596596)
  • Study revealed that betaIII spectrin was weakly stained or lost in most poorly differentiated hepatocellular carcinoma (HCC) cases but retained moderate to strong stain in most cholangiocarcinoma (CC) cases. These findings suggest, for the first time, that betaIII spectrins could be helpful in differentiating poorly differentiated HCC from CC. (PMID:30798076)
  • Two novel missense variants in SPTBN2 likely associated with spinocerebellar ataxia type 5. (PMID:33797620)
  • Expanding the beta-III Spectrin-Associated Phenotypes toward Non-Progressive Congenital Ataxias with Neurodegeneration. (PMID:33801522)
  • SPTBN2 Promotes the Progression of Thyroid Cancer by Accelerating G1/S Transition and Inhibiting Apoptosis. (PMID:35968508)
  • Increased Actin Binding Is a Shared Molecular Consequence of Numerous SCA5 Mutations in beta-III-Spectrin. (PMID:37626910)
  • SPTBN2 suppresses ferroptosis in NSCLC cells by facilitating SLC7A11 membrane trafficking and localization. (PMID:38241838)
  • SPTBN2 regulated by miR-214-3p inhibits the proliferation and migration of colorectal cancer cells. (PMID:38279463)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriosptbn2ENSDARG00000053956
mus_musculusSptbn2ENSMUSG00000067889
rattus_norvegicusSptbn2ENSRNOG00000058842

Paralogs (36): SYNE2 (ENSG00000054654), SPTB (ENSG00000070182), ACTN1 (ENSG00000072110), ACTN2 (ENSG00000077522), DSP (ENSG00000096696), DRP2 (ENSG00000102385), SPTBN1 (ENSG00000115306), MACF1 (ENSG00000127603), FLNC (ENSG00000128591), ACTN4 (ENSG00000130402), SYNE1 (ENSG00000131018), MICAL2 (ENSG00000133816), DTNA (ENSG00000134769), MICAL1 (ENSG00000135596), FLNB (ENSG00000136068), SPTBN5 (ENSG00000137877), DTNB (ENSG00000138101), GAS2L3 (ENSG00000139354), DST (ENSG00000151914), UTRN (ENSG00000152818), SPTBN4 (ENSG00000160460), SPTA1 (ENSG00000163554), CLMN (ENSG00000165959), PKHD1 (ENSG00000170927), SYNE3 (ENSG00000176438), PLEC (ENSG00000178209), SMTNL2 (ENSG00000188176), FLNA (ENSG00000196924), SPTAN1 (ENSG00000197694), DMD (ENSG00000198947), PKHD1L1 (ENSG00000205038), DYTN (ENSG00000232125), MICAL3 (ENSG00000243156), ACTN3 (ENSG00000248746), EPPK1 (ENSG00000261150), GAS2L2 (ENSG00000270765)

Protein

Protein identifiers

Spectrin beta chain, non-erythrocytic 2O15020 (reviewed: O15020)

Alternative names: Beta-III spectrin, Spinocerebellar ataxia 5 protein

All UniProt accessions (8): O15020, A0A087WYQ1, A0AAQ5BGS8, A0AAQ5BGT4, A0AAQ5BGT9, A0AAQ5BGU2, A0AAQ5BGW1, A4QPE4

UniProt curated annotations — full annotation on UniProt →

Function. Probably plays an important role in neuronal membrane skeleton.

Subcellular location. Cytoplasm. Cytoskeleton. Cell cortex.

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

Disease relevance. 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. The disease is caused by variants affecting the gene represented in this entry. Spinocerebellar ataxia, autosomal recessive, 14 (SCAR14) [MIM:615386] A form of spinocerebellar ataxia, 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. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the spectrin family.

Isoforms (2)

UniProt IDNamesCanonical?
O15020-11yes
O15020-22

RefSeq proteins (2): NP_001397954, NP_008877* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001589Actinin_actin-bd_CSConserved_site
IPR001605PH_dom-spectrin-typeDomain
IPR001715CH_domDomain
IPR001849PH_domainDomain
IPR002017Spectrin_repeatRepeat
IPR011993PH-like_dom_sfHomologous_superfamily
IPR016343Spectrin_bsuFamily
IPR018159Spectrin/alpha-actininRepeat
IPR036872CH_dom_sfHomologous_superfamily
IPR041681PH_9Domain

Pfam: PF00307, PF00435, PF15410

UniProt features (68 total): repeat 17, strand 12, modified residue 9, sequence variant 8, helix 6, turn 4, domain 3, region of interest 3, compositionally biased region 3, initiator methionine 1, chain 1, splice variant 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
6ANUELECTRON MICROSCOPY7
1WJMSOLUTION NMR
1WYQSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O15020-F176.910.08

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (9): 2, 6, 31, 959, 1073, 2171, 2199, 2354, 2359

Function

Pathways and Gene Ontology

Reactome pathways

21 pathways

IDPathway
R-HSA-2132295MHC class II antigen presentation
R-HSA-375165NCAM signaling for neurite out-growth
R-HSA-445095Interaction between L1 and Ankyrins
R-HSA-5673001RAF/MAP kinase cascade
R-HSA-6807878COPI-mediated anterograde transport
R-HSA-1266738Developmental Biology
R-HSA-1280218Adaptive Immune System
R-HSA-162582Signal Transduction
R-HSA-168256Immune System
R-HSA-199977ER to Golgi Anterograde Transport
R-HSA-199991Membrane Trafficking
R-HSA-373760L1CAM interactions
R-HSA-392499Metabolism of proteins
R-HSA-422475Axon guidance
R-HSA-446203Asparagine N-linked glycosylation
R-HSA-5653656Vesicle-mediated transport
R-HSA-5683057MAPK family signaling cascades
R-HSA-5684996MAPK1/MAPK3 signaling
R-HSA-597592Post-translational protein modification
R-HSA-948021Transport to the Golgi and subsequent modification
R-HSA-9675108Nervous system development

MSigDB gene sets: 289 (showing top): GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_ASSEMBLY, GOBP_HINDBRAIN_DEVELOPMENT, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_METENCEPHALON_DEVELOPMENT, GOBP_BEHAVIOR, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_SYNAPSE_ASSEMBLY, GOBP_ADULT_BEHAVIOR, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_POLYMERIZATION, GOZGIT_ESR1_TARGETS_DN, GOBP_GROWTH, REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH, GOBP_CEREBELLAR_CORTEX_MORPHOGENESIS, GOBP_NEGATIVE_REGULATION_OF_ACTIN_FILAMENT_DEPOLYMERIZATION

GO Biological Process (10): synapse assembly (GO:0007416), vesicle-mediated transport (GO:0016192), cerebellar Purkinje cell layer morphogenesis (GO:0021692), actin cytoskeleton organization (GO:0030036), adult behavior (GO:0030534), multicellular organism growth (GO:0035264), actin filament capping (GO:0051693), regulation of postsynaptic specialization assembly (GO:0099150), cytoskeleton organization (GO:0007010), postsynapse organization (GO:0099173)

GO Molecular Function (9): actin binding (GO:0003779), structural constituent of cytoskeleton (GO:0005200), phospholipid binding (GO:0005543), cadherin binding (GO:0045296), actin filament binding (GO:0051015), structural constituent of synapse (GO:0098918), structural constituent of postsynapse (GO:0099186), protein binding (GO:0005515), cytoskeletal protein binding (GO:0008092)

GO Cellular Component (18): obsolete extracellular space (GO:0005615), cytosol (GO:0005829), plasma membrane (GO:0005886), spectrin (GO:0008091), apical plasma membrane (GO:0016324), cell junction (GO:0030054), cortical actin cytoskeleton (GO:0030864), paranodal junction (GO:0033010), cell projection (GO:0042995), neuronal cell body (GO:0043025), parallel fiber to Purkinje cell synapse (GO:0098688), presynapse (GO:0098793), glutamatergic synapse (GO:0098978), postsynaptic spectrin-associated cytoskeleton (GO:0099189), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cell cortex (GO:0005938), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-15 pathways:

CategoryPathways
Axon guidance2
Adaptive Immune System1
L1CAM interactions1
MAPK1/MAPK3 signaling1
ER to Golgi Anterograde Transport1
Immune System1
Membrane Trafficking1
Transport to the Golgi and subsequent modification1
Vesicle-mediated transport1
Nervous system development1
Post-translational protein modification1
Signal Transduction1
MAPK family signaling cascades1
Metabolism of proteins1
Asparagine N-linked glycosylation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure6
synapse organization3
synapse3
cytoskeleton organization2
structural molecule activity2
postsynapse2
cytoplasm2
cell periphery2
nervous system development1
cell junction assembly1
transport1
cellular process1
anatomical structure morphogenesis1
cerebellar Purkinje cell layer development1
cerebellar cortex morphogenesis1
actin filament-based process1
behavior1
multicellular organismal process1
developmental growth1
negative regulation of actin filament depolymerization1
negative regulation of actin filament polymerization1
postsynaptic specialization assembly1
regulation of organelle assembly1
organelle organization1
cellular component organization1
cytoskeletal protein binding1
cytoskeleton1
lipid binding1
cell adhesion molecule binding1
actin binding1
protein-containing complex binding1
structural constituent of synapse1
postsynapse organization1
binding1
protein binding1
membrane1
cortical actin cytoskeleton1
protein-containing complex1
apical part of cell1
plasma membrane region1

Protein interactions and networks

STRING

1410 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SPTBN2SLC1A6P48664949
SPTBN2ATXN10Q9UBB4924
SPTBN2ARHGEF11O15085890
SPTBN2PLEKHG4Q58EX7878
SPTBN2TTBK2Q6IQ55876
SPTBN2ATXN7O15265827
SPTBN2CACNA1AP78510823
SPTBN2ZNF592Q92610818
SPTBN2GRID2O43424726
SPTBN2KCNC3Q14003726
SPTBN2ATXN3P54252683
SPTBN2ATXN1P54253670
SPTBN2EPB41P11171664
SPTBN2PRKCGP05129662
SPTBN2ATXN2Q99700661

IntAct

92 interactions, top by confidence:

ABTypeScore
IKBKGIKBKBpsi-mi:“MI:0914”(association)0.980
SMARCB1ARID1Apsi-mi:“MI:0914”(association)0.860
OPG044DDX3Xpsi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
KIFAP3KIF3Cpsi-mi:“MI:0914”(association)0.640
TUBB3POTEFpsi-mi:“MI:0914”(association)0.530
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
ESR2FBLL1psi-mi:“MI:0914”(association)0.460
ATAD2SPTBN2psi-mi:“MI:0915”(physical association)0.400
Cdk1psi-mi:“MI:0915”(physical association)0.400
SPTBN2ADRB2psi-mi:“MI:0915”(physical association)0.370
CELSR3SPTBN2psi-mi:“MI:0915”(physical association)0.370
SPTBN2psi-mi:“MI:0915”(physical association)0.370
SPTBN2psi-mi:“MI:0915”(physical association)0.370
SPTBN2BKRF1psi-mi:“MI:0915”(physical association)0.370
AurkbSPTBN2psi-mi:“MI:0914”(association)0.350
MYO18APLEKHG3psi-mi:“MI:0914”(association)0.350
MYO1CPLEKHG3psi-mi:“MI:0914”(association)0.350
MYO19PLEKHG3psi-mi:“MI:0914”(association)0.350
FLNAPLEKHG3psi-mi:“MI:0914”(association)0.350
Bod1SPTBN2psi-mi:“MI:0914”(association)0.350
Calml3PLEKHG3psi-mi:“MI:0914”(association)0.350
SYNPOLMO7psi-mi:“MI:0914”(association)0.350
Myh9PLEKHG3psi-mi:“MI:0914”(association)0.350
Myo1cPLEKHG3psi-mi:“MI:0914”(association)0.350
Myh9GOSR1psi-mi:“MI:0914”(association)0.350
CAPZA2PLEKHG3psi-mi:“MI:0914”(association)0.350

BioGRID (233): SPTBN2 (Affinity Capture-MS), SPTBN2 (Affinity Capture-MS), SPTBN2 (Co-fractionation), SPTBN2 (Co-fractionation), SPTBN2 (Co-fractionation), SPTBN2 (Co-fractionation), SPTBN2 (Co-fractionation), SPTBN2 (Affinity Capture-MS), SPTBN2 (Affinity Capture-MS), SPTBN2 (Affinity Capture-MS), SPTBN2 (Affinity Capture-MS), SPTBN2 (Affinity Capture-MS), SPTBN2 (Affinity Capture-MS), SPTBN2 (Affinity Capture-MS), SPTBN2 (Affinity Capture-MS)

ESM2 similar proteins: A5D7D1, B0WYY2, L7UZ85, O01422, O13728, O15020, O43707, O88990, P05094, P11277, P12814, P15311, P15508, P18091, P20111, P26040, P31976, P31977, P32599, P35609, P46150, P57780, Q00963, Q01082, Q08043, Q0III9, Q13576, Q2PFV7, Q3B7N2, Q3UQ44, Q3ZC55, Q4QR29, Q5RCS6, Q62018, Q62261, Q6DEU9, Q6NXC0, Q6PD62, Q7PKQ5, Q7TPR4

Diamond homologs: A5D7D1, D3ZEN0, D3ZHA0, D3ZHV2, D3ZQL6, E1BBG2, F1MF74, F1RA39, F6QZ15, G3MWR8, G3V7L1, L7UZ85, M9MRD1, O13728, O15020, O43707, O75369, O76329, O88990, O94851, O97592, P05094, P05095, P07751, P11277, P11530, P11531, P11532, P11533, P12814, P13395, P13466, P15508, P16086, P16546, P18091, P20111, P21333, P30427, P35609

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 99 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Signaling by FLT3 fusion proteins546.8×1e-05
RAF activation527.5×5e-05
Signaling by high-kinase activity BRAF mutants526.0×6e-05
Signaling by FGFR1 in disease524.0×6e-05
MAP2K and MAPK activation523.4×7e-05
Signaling by RAF1 mutants522.8×7e-05
Signaling by moderate kinase activity BRAF mutants520.8×9e-05
Paradoxical activation of RAF signaling by kinase inactive BRAF520.8×9e-05

GO biological processes:

GO termPartnersFoldFDR
microtubule cytoskeleton organization710.1×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

1407 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic25
Likely pathogenic28
Uncertain significance665
Likely benign352
Benign64

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1027424NM_006946.4(SPTBN2):c.157+1G>APathogenic
1048078NM_006946.4(SPTBN2):c.1240C>T (p.Arg414Cys)Pathogenic
1074233NM_006946.4(SPTBN2):c.5352dup (p.Asp1785Ter)Pathogenic
1323650NM_006946.4(SPTBN2):c.1444C>T (p.Gln482Ter)Pathogenic
1879205NM_006946.4(SPTBN2):c.6722+1G>TPathogenic
1879208NM_006946.4(SPTBN2):c.3301G>T (p.Glu1101Ter)Pathogenic
208740NM_006946.4(SPTBN2):c.1915G>T (p.Glu639Ter)Pathogenic
2258160NM_006946.4(SPTBN2):c.2250_2252del (p.Tyr750_Gln751delinsTer)Pathogenic
2500212NM_006946.4(SPTBN2):c.5581del (p.Asp1861fs)Pathogenic
2642007NM_006946.4(SPTBN2):c.158-1G>TPathogenic
2734018NM_006946.4(SPTBN2):c.1121G>T (p.Ser374Ile)Pathogenic
2810551NM_006946.4(SPTBN2):c.4233C>A (p.Tyr1411Ter)Pathogenic
2835724NM_006946.4(SPTBN2):c.4801_4816del (p.Glu1601fs)Pathogenic
3237165NM_006946.4(SPTBN2):c.6304G>T (p.Glu2102Ter)Pathogenic
3244770NC_000011.9:g.(?66472049)(66473328_?)delPathogenic
3391810NM_006946.4(SPTBN2):c.3436C>T (p.Arg1146Ter)Pathogenic
3392612NM_006946.4(SPTBN2):c.6034+1G>APathogenic
4085932NM_006946.4(SPTBN2):c.3867+1G>CPathogenic
448482NM_006946.4(SPTBN2):c.1596_1634del (p.Glu532_Met544del)Pathogenic
4811994NM_006946.4(SPTBN2):c.5197C>T (p.Arg1733Ter)Pathogenic
5274NM_006946.4(SPTBN2):c.1886_1900del (p.Leu629_Arg634delinsTrp)Pathogenic
5275NM_006946.4(SPTBN2):c.758T>C (p.Leu253Pro)Pathogenic
620423NM_006946.4(SPTBN2):c.5515C>T (p.Gln1839Ter)Pathogenic
64367NM_006946.4(SPTBN2):c.1881C>A (p.Cys627Ter)Pathogenic
64369NM_006946.4(SPTBN2):c.2864_2868del (p.Thr955fs)Pathogenic
1029115NM_006946.4(SPTBN2):c.4358A>T (p.Asp1453Val)Likely pathogenic
1029118NM_006946.4(SPTBN2):c.812C>T (p.Thr271Ile)Likely pathogenic
1195160NM_006946.4(SPTBN2):c.793G>C (p.Asp265His)Likely pathogenic
1333225NM_006946.4(SPTBN2):c.5974C>T (p.Gln1992Ter)Likely pathogenic
1485369NM_006946.4(SPTBN2):c.5950-2A>CLikely pathogenic

SpliceAI

5256 predictions. Top by Δscore:

VariantEffectΔscore
11:66687020:T:Adonor_gain1.0000
11:66687421:CTGTA:Cdonor_loss1.0000
11:66687422:TGTAC:Tdonor_loss1.0000
11:66687423:GTACC:Gdonor_loss1.0000
11:66687424:TACCT:Tdonor_loss1.0000
11:66687426:C:CTdonor_loss1.0000
11:66687643:GGTCC:Gacceptor_gain1.0000
11:66687644:GTCC:Gacceptor_gain1.0000
11:66687645:TCC:Tacceptor_gain1.0000
11:66687646:CC:Cacceptor_gain1.0000
11:66687646:CCC:Cacceptor_gain1.0000
11:66687647:CC:Cacceptor_gain1.0000
11:66687648:C:CCacceptor_gain1.0000
11:66687648:C:Tacceptor_gain1.0000
11:66687648:CTGG:Cacceptor_loss1.0000
11:66687860:GAACT:Gdonor_loss1.0000
11:66687861:AACT:Adonor_loss1.0000
11:66687863:CTC:Cdonor_loss1.0000
11:66687864:TCA:Tdonor_loss1.0000
11:66687865:CA:Cdonor_loss1.0000
11:66687866:A:ACdonor_gain1.0000
11:66687867:C:CCdonor_gain1.0000
11:66688080:C:CCacceptor_gain1.0000
11:66688090:C:CTacceptor_gain1.0000
11:66688091:A:Tacceptor_gain1.0000
11:66688860:C:CTacceptor_gain1.0000
11:66688861:G:Tacceptor_gain1.0000
11:66689090:GCTCA:Gdonor_loss1.0000
11:66689091:CTCA:Cdonor_loss1.0000
11:66689092:TCA:Tdonor_loss1.0000

AlphaMissense

15544 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:66687465:C:AK2228N1.000
11:66687465:C:GK2228N1.000
11:66708265:C:GR409P1.000
11:66708278:C:GA405P1.000
11:66708286:A:GL402P1.000
11:66708294:C:AW399C1.000
11:66708294:C:GW399C1.000
11:66708296:A:GW399R1.000
11:66708296:A:TW399R1.000
11:66708983:G:CF370L1.000
11:66708983:G:TF370L1.000
11:66708984:A:GF370S1.000
11:66708985:A:GF370L1.000
11:66709007:T:AK362N1.000
11:66709007:T:GK362N1.000
11:66709016:A:CF359L1.000
11:66709016:A:TF359L1.000
11:66709018:A:GF359L1.000
11:66710705:A:GL317P1.000
11:66710973:A:CY277D1.000
11:66713642:A:GL254P1.000
11:66713693:A:GL237P1.000
11:66714109:G:TA213D1.000
11:66714110:C:GA213P1.000
11:66714115:A:GF211S1.000
11:66714124:C:AG208V1.000
11:66714124:C:TG208E1.000
11:66714125:C:GG208R1.000
11:66714125:C:TG208R1.000
11:66714133:C:GW205S1.000

dbSNP variants (sampled 300 via entrez): RS1000022170 (11:66714846 G>T), RS1000153610 (11:66719698 G>A,T), RS1000162991 (11:66708120 C>A,T), RS1000230616 (11:66733847 A>G), RS1000246907 (11:66704147 T>C), RS1000256259 (11:66740453 C>T), RS1000290073 (11:66702062 T>C), RS1000366628 (11:66746253 G>C), RS1000383114 (11:66701865 T>A,C), RS1000457991 (11:66720536 C>A,T), RS1000482048 (11:66704303 G>A,T), RS1000557426 (11:66716126 G>A), RS1000672558 (11:66725881 T>C), RS1000673652 (11:66691153 C>T), RS1000757791 (11:66686157 C>T)

Disease associations

OMIM: gene MIM:604985 | disease phenotypes: MIM:600224, MIM:615386, MIM:303350

GenCC curated gene-disease

DiseaseClassificationInheritance
spinocerebellar ataxia type 5DefinitiveAutosomal dominant
autosomal recessive spinocerebellar ataxia 14DefinitiveAutosomal recessive

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
autosomal recessive spinocerebellar ataxia 14DefinitiveAR
spinocerebellar ataxia type 5DefinitiveAD

Mondo (6): spinocerebellar ataxia type 5 (MONDO:0010848), autosomal recessive spinocerebellar ataxia 14 (MONDO:0014159), hereditary spastic paraplegia (MONDO:0019064), cerebellar ataxia (MONDO:0000437), hereditary ataxia (MONDO:0100309), intellectual disability (MONDO:0001071)

Orphanet (6): Spinocerebellar ataxia type 5 (Orphanet:98766), Spectrin-associated autosomal recessive cerebellar ataxia (Orphanet:352403), Hereditary spastic paraplegia (Orphanet:685), Rare ataxia (Orphanet:102002), Hereditary ataxia (Orphanet:183518), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

45 total (30 of 45 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000317Facial myokymia
HP:0000486Strabismus
HP:0000571Hypometric saccades
HP:0000639Nystagmus
HP:0000640Gaze-evoked nystagmus
HP:0000641Dysmetric saccades
HP:0000651Diplopia
HP:0000666Horizontal nystagmus
HP:0000750Delayed speech and language development
HP:0001251Ataxia
HP:0001252Hypotonia
HP:0001256Mild intellectual disability
HP:0001257Spasticity
HP:0001260Dysarthria
HP:0001263Global developmental delay
HP:0001270Motor delay
HP:0001272Cerebellar atrophy
HP:0001288Gait disturbance
HP:0001310Dysmetria
HP:0001321Cerebellar hypoplasia
HP:0001347Hyperreflexia
HP:0001350Slurred speech
HP:0001583Rotary nystagmus
HP:0002066Gait ataxia
HP:0002070Limb ataxia
HP:0002073Progressive cerebellar ataxia
HP:0002075Dysdiadochokinesis
HP:0002078Truncal ataxia

GWAS associations

6 associations (top):

StudyTraitp-value
GCST001241_12Bipolar disorder2.000000e-07
GCST004139_3Bipolar disorder1.000000e-07
GCST008103_30Bipolar disorder4.000000e-08
GCST012090_40Major depressive disorder (MTAG)2.000000e-08
GCST012227_667Hip circumference adjusted for BMI1.000000e-09
GCST90020028_1912Hip circumference adjusted for BMI7.000000e-27

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0008039BMI-adjusted hip circumference

MeSH disease descriptors (4)

DescriptorNameTree numbers
D002524Cerebellar AtaxiaC10.228.140.252.190; C10.597.350.090.500; C23.888.592.350.090.200
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D015419Spastic Paraplegia, HereditaryC10.500.300.820; C10.574.500.495.820; C10.668.829.800.300.820; C16.131.666.300.820; C16.320.400.375.820
C531684Hereditary spinal ataxia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aincreases expression, decreases expression, decreases reaction, increases abundance2
sodium arseniteaffects methylation, increases expression2
(+)-JQ1 compounddecreases expression2
Arsenicaffects methylation, increases methylation2
Aflatoxin B1increases methylation, decreases methylation2
FR900359decreases phosphorylation1
ginger extractdecreases reaction, increases abundance, increases expression1
dicrotophosincreases expression1
2,4,6-tribromophenoldecreases expression1
pirinixic acidaffects binding, increases activity, increases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, decreases expression, affects localization1
decabromobiphenyl etherdecreases expression1
tetrabromobisphenol Adecreases expression1
benzo(e)pyrenedecreases methylation1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic acidincreases expression1
abrinedecreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
hexabrominated diphenyl ether 153increases expression1
Sunitinibdecreases expression1
Cadmiumincreases expression1
Calcitriolincreases expression1
Cisplatindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Furaldehydeaffects cotreatment, decreases expression, affects localization, increases expression1
Ivermectinincreases expression1
Methapyrilenedecreases methylation1
Oils, Volatiledecreases reaction, increases abundance, increases expression1
Sodium Chlorideaffects cotreatment, decreases expression, affects localization, increases expression1

Cellosaurus cell lines

1 cell lines: 1 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E7NRKOLF2.1J SPTBN2 25.2kbdel DEL/DELInduced pluripotent stem cellMale

Clinical trials (associated diseases)

287 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT07542548PHASE4COMPLETEDD-Cycloserine for Serine Palmitoyltransferase Inhibition
NCT00950196PHASE4COMPLETEDAmantadine for Improving Neurologic Symptoms in Ataxia-Telangiectasia
NCT04107740PHASE4COMPLETEDC-Trelin Orally Disintegrated(OD) Tablet 5mg in Ataxia Due to Spinocerebellar Degeneration
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT01970098PHASE3COMPLETEDA Confirmatory Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970111PHASE3COMPLETEDAn Extension Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970124PHASE3COMPLETEDA Long-Term Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970137PHASE3COMPLETEDA 24-week Open-label Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT02889302PHASE3COMPLETEDAn Additional Confirmatory Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT03408080PHASE3ACTIVE_NOT_RECRUITINGOpen Pilot Trial of BHV-4157
NCT03701399PHASE3ACTIVE_NOT_RECRUITINGTroriluzole in Adult Participants With Spinocerebellar Ataxia
NCT03901638PHASE3TERMINATEDTllsh2910 for Ataxia and Gut Microbiota Alteration in Patients of Multiple System Atrophy
NCT07040137PHASE3RECRUITINGConfirmatory Study 3 of KPS-0373 in Patients With Spinocerebellar Degeneration
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT03961906PHASE2COMPLETEDPhysiotherapy in Hereditary Spastic Paraplegia
NCT04768166PHASE2COMPLETEDTesting Miglustat Administration in Subjects With Spastic Paraplegia 11
NCT00034242PHASE2COMPLETEDHigh-Dose Intravenous Immunoglobulin to Treat Cerebellar Degeneration
NCT00202397PHASE2COMPLETEDEffect of Riluzole as a Symptomatic Approach in Patients With Chronic Cerebellar Ataxia
NCT00863538PHASE2COMPLETEDPhase II Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01004016PHASE2COMPLETEDA Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01350440PHASE2COMPLETEDSafety and Efficacy of Intravenous Immune Globulin in Treating Spinocerebellar Ataxia
NCT02540655PHASE2COMPLETEDEfficacy and Safety Study of Stemchymal® in Polyglutamine Spinocerebellar Ataxia
NCT03932669PHASE2COMPLETEDEffect of Nilotinib in Cerebellar Ataxia Patients
NCT04301284PHASE2WITHDRAWNStudy of CAD-1883 for Spinocerebellar Ataxia
NCT05125666PHASE2UNKNOWNEfficacy of Dual Task Training on Children With Ataxia After Medulloblastoma Resection
NCT06397274PHASE2NOT_YET_RECRUITINGStemchymal® for Polyglutamine Spinocerebellar Ataxia
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT06117020PHASE1COMPLETEDSingle and Multiple Ascending Dose Study of MTR-601 in Healthy Individuals
NCT00683943PHASE1COMPLETEDLithium Treatment for Patients With Spinocerebellar Ataxia Type I
NCT02287064PHASE1UNKNOWNAn Open-label Trial of Intravenous Immune Globulin (IVIG)in Treating Spinocerebellar Ataxias
NCT05157802PHASE1ACTIVE_NOT_RECRUITINGPromoting Physical Activity Engagement for People With Early-stage Cerebellar Ataxia
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism