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GeneE
25 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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SPTAN1
spectrin alpha, non-erythrocytic 1
Chromosome 9 · 9q34.11
NCBI Gene: 6709Ensembl: ENSG00000197694.19HGNC: HGNC:11273UniProt: A0A0D9SF54
340PubMed Papers
24Diseases
0Drugs
133Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
RESEARCH IMPACT
Highly StudiedTrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
cadherin bindingextracellular exosomeextracellular vesicleprotein bindingdevelopmental and epileptic encephalopathy, 5developmental and epileptic encephalopathyneuronopathy, distal hereditary motor, autosomal dominant 11genetic disorder
✦AI Summary

SPTAN1 encodes αII-spectrin, a cytoskeletal protein essential for cellular structure and neuronal function. As a key component of the spectrin-based membrane skeleton, SPTAN1 binds to actin filaments and plasma membrane proteins, providing structural support and proper localization of membrane components 1. The protein functions through a haploinsufficiency mechanism, as loss-of-function variants cause neurological disorders 1. SPTAN1 also acts as a cell density sensor by recruiting NUMB proteins when phosphorylated at high cell density, which activates Hippo signaling to prevent oncogenesis through contact inhibition 2. Pathogenic variants in SPTAN1 cause a broad spectrum of neurological disorders, including three distinct phenotypic groups: developmental epileptic encephalopathy, milder developmental delay with or without seizures, and pure or complex hereditary spastic paraplegia/ataxia 34. The protein is critical for neurodevelopment, and variants are associated with intellectual disability, autism, and motor neuropathies 15. Recent studies also reveal SPTAN1's role in cancer, where lactylation modifications promote hepatocellular carcinoma progression by activating NOTCH1/HES1 signaling and immune suppression 6. These findings establish SPTAN1 as both a crucial neuronal organizer and potential therapeutic target.

Sources cited
1
SPTAN1 encodes αII-spectrin cytoskeletal protein and functions through haploinsufficiency mechanism causing intellectual disability and autism
PMID: 33847457
2
SPTAN1 acts as cell density sensor through phosphorylation and NUMB recruitment to activate Hippo signaling for contact inhibition
PMID: 37843276
3
SPTAN1 variants cause three distinct phenotypic groups including epileptic encephalopathy, developmental delay, and spastic paraplegia/ataxia
PMID: 36331550
4
SPTAN1 mutations cause spastic paraplegia and cerebellar ataxia through disruption of spectrin helix interlinking
PMID: 35150594
5
SPTAN1 is involved in hereditary motor neuropathies pathogenesis
PMID: 32796276
6
Lactylated SPTAN1 promotes hepatocellular carcinoma through NOTCH1/HES1 activation and immune suppression
PMID: 41243220
Disease Associationsⓘ24
developmental and epileptic encephalopathy, 5Open Targets
0.77Strong
developmental and epileptic encephalopathyOpen Targets
0.65Moderate
neuronopathy, distal hereditary motor, autosomal dominant 11Open Targets
0.53Moderate
genetic disorderOpen Targets
0.52Moderate
developmental delay with or without epilepsyOpen Targets
0.51Moderate
spastic paraplegia 91, autosomal dominant, with or without cerebellar ataxiaOpen Targets
0.45Moderate
hereditary spastic paraplegiaOpen Targets
0.43Moderate
Rolandic epilepsyOpen Targets
0.42Moderate
self-limited epilepsy with centrotemporal spikesOpen Targets
0.42Moderate
infantile spasmsOpen Targets
0.37Weak
distal hereditary motor neuropathyOpen Targets
0.37Weak
genetic developmental and epileptic encephalopathyOpen Targets
0.37Weak
neurodegenerative diseaseOpen Targets
0.36Weak
Epileptic encephalopathyOpen Targets
0.34Weak
Neurodevelopmental abnormalityOpen Targets
0.34Weak
Neurodevelopmental disorderOpen Targets
0.30Weak
neuromuscular diseaseOpen Targets
0.30Weak
partial epilepsyOpen Targets
0.27Weak
spastic ataxiaOpen Targets
0.27Weak
syndromic X-linked intellectual disability Raymond typeOpen Targets
0.27Weak
Developmental and epileptic encephalopathy 5UniProt
Developmental delay with or without epilepsyUniProt
Neuronopathy, distal hereditary motor, autosomal dominant 11UniProt
Spastic paraplegia 91, autosomal dominant, with or without cerebellar ataxiaUniProt
Pathogenic Variants133
NM_001130438.3(SPTAN1):c.6241AAG[2] (p.Lys2083del)Pathogenic
Spastic paraplegia 91, autosomal dominant, with or without cerebellar ataxia|not provided|Developmental and epileptic encephalopathy, 5|Early-infantile DEE
★★☆☆2026→ Residue 2083
NM_001130438.3(SPTAN1):c.6922C>T (p.Arg2308Cys)Pathogenic
Developmental and epileptic encephalopathy, 5|not provided|Early-infantile DEE
★★☆☆2025→ Residue 2308
NM_001130438.3(SPTAN1):c.6899ACCAGCTGG[3] (p.2300DQL[3])Pathogenic
Developmental and epileptic encephalopathy, 5|not provided|Undetermined early-onset epileptic encephalopathy|not specified|Inborn genetic diseases|SPTAN1-related disorder|Early-infantile DEE
★★☆☆2025
NM_001130438.3(SPTAN1):c.6031C>T (p.Arg2011Ter)Pathogenic
not provided|Hereditary spastic paraplegia
★★☆☆2025→ Residue 2011
NM_001130438.3(SPTAN1):c.6899ACCAGCTGG[1] (p.2300DQL[1])Pathogenic
not provided|Focal epilepsy|See cases|Developmental and epileptic encephalopathy, 5|Developmental delay with or without epilepsy|SPTAN1-related disorder|Early-infantile DEE
★★☆☆2025
NM_001130438.3(SPTAN1):c.3014G>A (p.Trp1005Ter)Pathogenic
Developmental and epileptic encephalopathy, 5
★★☆☆2025→ Residue 1005
NM_001130438.3(SPTAN1):c.415C>T (p.Arg139Ter)Likely pathogenic
Developmental and epileptic encephalopathy, 5|Neuronopathy, distal hereditary motor, autosomal dominant 11|Spastic paraplegia 91, autosomal dominant, with or without cerebellar ataxia
★★☆☆2025→ Residue 139
NM_001130438.3(SPTAN1):c.3388C>T (p.Gln1130Ter)Pathogenic
Neuronopathy, distal hereditary motor, autosomal dominant 11|Inborn genetic diseases
★★☆☆2025→ Residue 1130
NM_001130438.3(SPTAN1):c.1879C>T (p.Arg627Ter)Pathogenic
not provided
★★☆☆2025→ Residue 627
NM_001130438.3(SPTAN1):c.466C>T (p.Arg156Ter)Pathogenic
Developmental delay with or without epilepsy;Neuronopathy, distal hereditary motor, autosomal dominant 11|Developmental and epileptic encephalopathy, 5|Neurodevelopmental abnormality|not provided
★★☆☆2025→ Residue 156
NM_001130438.3(SPTAN1):c.133C>T (p.Arg45Ter)Pathogenic
not provided
★★☆☆2025→ Residue 45
NM_001130438.3(SPTAN1):c.6811G>A (p.Glu2271Lys)Pathogenic
not provided|Developmental and epileptic encephalopathy, 5|Early-infantile DEE
★★☆☆2024→ Residue 2271
NM_001130438.3(SPTAN1):c.1642C>T (p.Arg548Ter)Pathogenic
not provided|Early-infantile DEE
★★☆☆2024→ Residue 548
NM_001130438.3(SPTAN1):c.6616GAG[1] (p.Glu2207del)Pathogenic
Developmental and epileptic encephalopathy, 5|not provided|SPTAN1-related disorder|Early-infantile DEE
★★☆☆2024→ Residue 2207
NM_001130438.3(SPTAN1):c.6019_6020del (p.Thr2006_Asp2007insTer)Pathogenic
SPTAN1-related disorder|Early-infantile DEE
★★☆☆2023→ Residue 2006
NM_001130438.3(SPTAN1):c.4828C>T (p.Arg1610Trp)Pathogenic
not provided|Developmental and epileptic encephalopathy, 5|Congenital cerebellar hypoplasia|SPTAN1-related disorder
★★☆☆2023→ Residue 1610
NM_001130438.3(SPTAN1):c.6592_6597dup (p.Leu2198_Gln2199dup)Likely pathogenic
Developmental and epileptic encephalopathy, 5|Early-infantile DEE
★★☆☆2023→ Residue 2198
NM_001130438.3(SPTAN1):c.6917GCATGC[3] (p.Arg2308_Met2309dup)Pathogenic
not provided|Epileptic encephalopathy|Developmental and epileptic encephalopathy, 5
★★☆☆2022→ Residue 2308
NM_001130438.3(SPTAN1):c.3227del (p.Leu1076fs)Likely pathogenic
Developmental delay with or without epilepsy
★☆☆☆2026→ Residue 1076
NM_001130438.3(SPTAN1):c.428_431del (p.Ile143fs)Likely pathogenic
Autosomal dominant SPTAN1-related disorders
★☆☆☆2025→ Residue 143
View on ClinVar ↗
Related Genes
FLNBShared pathway100%SMTNL2Shared pathway100%THSD7AShared pathway100%PHACTR3Shared pathway100%SPECC1Shared pathway100%THSD7BShared pathway100%
Tissue Expression6 tissues
Brain
100%
Heart
53%
Ovary
38%
Bone Marrow
32%
Lung
31%
Liver
18%
Gene Interaction Network
Click a node to explore
SPTAN1FLNBSMTNL2THSD7APHACTR3SPECC1THSD7B
PROTEIN STRUCTURE
Preparing viewer…
PDB6ZEH · 1.30 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.22Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.18 [0.14–0.22]
RankingsWhere SPTAN1 stands among ~20K protein-coding genes
  • #949of 20,598
    Most Researched340 · top 5%
  • #579of 5,498
    Most Pathogenic Variants133 · top quartile
  • #573of 17,882
    Most Constrained (LOEUF)0.22 · top 5%
Genes detectedSPTAN1
Sources retrieved25 papers
Response time—
📄 Sources
25▼
1
Heterozygous variants in SPTBN1 cause intellectual disability and autism.
PMID: 33847457
Am J Med Genet A · 2021
1.00
2
A 20-year Clinical and Genetic Neuromuscular Cohort Analysis in Lebanon: An International Effort.
PMID: 34602496
J Neuromuscul Dis · 2022
0.90
3
Expanding SPTAN1 monoallelic variant associated disorders: From epileptic encephalopathy to pure spastic paraplegia and ataxia.
PMID: 36331550
Genet Med · 2023
0.80
4
Epileptic encephalopathies and progressive neurodegeneration.
PMID: 38582661
Rev Neurol (Paris) · 2024
0.76
5
SPTAN1/NUMB axis senses cell density to restrain cell growth and oncogenesis through Hippo signaling.
PMID: 37843276
J Clin Invest · 2023
0.70