SPTAN1

Chr 9AD

spectrin alpha, non-erythrocytic 1

Also known as: DEE5, DEVEP, EIEE5, HMN11, HMND11, NEAS, SPG91, SPTA2

The protein functions as a cytoskeletal scaffold protein that stabilizes the plasma membrane and organizes intracellular organelles, and is also involved in DNA repair and cell cycle regulation. Mutations cause a spectrum of autosomal dominant neurological disorders including developmental and epileptic encephalopathy, developmental delay with or without epilepsy, distal hereditary motor neuronopathy, and spastic paraplegia with or without cerebellar ataxia. The gene is highly intolerant to loss-of-function variants, and mutations can cause disease predominantly through haploinsufficiency, though the broad phenotypic spectrum suggests variant-dependent mechanisms may contribute.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
DNmechanismADLOEUF 0.104 OMIM phenotypes
Clinical SummarySPTAN1
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Gene-Disease Validity (ClinGen)
developmental and epileptic encephalopathy · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
📖
GeneReview available — SPTAN1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.10LOEUF
pLI 1.000
Z-score 10.47
OE 0.06 (0.030.10)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
5.52Z-score
OE missense 0.58 (0.550.62)
802 obs / 1379.2 exp
Constrained

Extremely missense-constrained (top ~0.01%)

Observed / Expected Ratios
LoF OE0.06 (0.030.10)
00.351.4
Missense OE0.58 (0.550.62)
00.61.4
Synonymous OE1.07
01.21.6
LoF obs/exp: 8 / 143.2Missense obs/exp: 802 / 1379.2Syn Z: -1.25
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveSPTAN1-related neurodevelopmental disorder with epilepsy and spastic paraplegiaDNAD
DN
0.5477th %ile
GOF
0.6737th %ile
LOF
0.51top 25%

This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function, gain-of-function and dominant-negative). The Badonyi & Marsh model scores gain-of-function highest among its predictions, but genomic evidence (constraint, ClinVar variant spectrum, and literature) most strongly supports loss-of-function (haploinsufficiency). Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

LOFLOEUF 0.10
GOFprediction above median
DN1 literature citation

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Literature Evidence

DNaken together, these findings implicate aII spectrin in critical aspects of dendritic and axonal development and synaptogenesis, and support a dominant-negative mechanism of SPTAN1 mutations in EIEE5.PMID:29337302

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SPTAN1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC