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Mendeliome

Gene: SPTAN1

Green List (high evidence)

SPTAN1 (spectrin alpha, non-erythrocytic 1)
EnsemblGeneIds (GRCh38): ENSG00000197694
EnsemblGeneIds (GRCh37): ENSG00000197694
OMIM: 182810, Gene2Phenotype
SPTAN1 is in 11 panels

4 reviews

Bryony Thompson (Royal Melbourne Hospital)

Green List (high evidence)

20 cases from 14 families with early childhood onset distal myopathy with heterozygous loss of function variants.
Created: 3 Mar 2025, 9:28 a.m. | Last Modified: 3 Mar 2025, 9:28 a.m.
Panel Version: 1.2335

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
distal myopathy MONDO:0018949

Publications

Variants in this GENE are reported as part of current diagnostic practice

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Green List (high evidence)

PMID 36331550: further 31 individuals reported with mono-allelic variants. Three phenotypes observed:
1. DEE
2. Isolated DD/ID
3. HSP or ataxia
Created: 28 Nov 2022, 1:14 a.m. | Last Modified: 28 Nov 2022, 1:14 a.m.
Panel Version: 1.486
Leveille et al (2019) - 2 patients with HSP with biallelic missense SPTAN1 variants Previously described zebrafish, mouse, and rat animal models of SPTAN1 deficiency, all consistently showing axonal degeneration, fitting the pathological features of HSP in humans. Xie et al (2022) - 1 patient with complicated HSP and homozygous SPTAN1 mutation. Healthy parents and sister all carried the heterozygous mutation. Van de Vondel et al (2022) - 22 patients from 14 families with five novel heterozygous SPTAN1 variants. Presentations ranged from cerebellar ataxia, intellectual disability, epilepsy, and spastic paraplegia. A recurrent missense mutation (p.Arg19Trp) in 15 patients with spastic paraplegia. Through protein modeling they showed that mutated amino acids are located at crucial interlinking positions, interconnecting the three-helix bundle of a spectrin repeat.
Created: 30 May 2022, 7:52 a.m. | Last Modified: 30 May 2022, 7:52 a.m.
Panel Version: 1.28
At least 4 unrelated families reported with DEE phenotype.
Created: 1 Mar 2021, 9:51 a.m. | Last Modified: 1 Mar 2021, 9:55 a.m.
Panel Version: 0.6513

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Phenotypes
Developmental and epileptic encephalopathy 5, MIM# 613477; Hereditary spastic paraplegia MONDO:0019064, SPTAN1-related; Neuronopathy, distal hereditary motor, 11, autosomal dominant, MIM# 620528; Autosomal dominant spastic paraplegia-91, with or without cerebellar ataxia (SPG91), MIM#620538

Publications

Alison Yeung (Victorian Clinical Genetics Services)

Comment on mode of inheritance: phenotype expansion
Created: 1 Mar 2021, 5:06 a.m. | Last Modified: 1 Mar 2021, 5:06 a.m.
Panel Version: 0.6500

Melanie Marty (Victorian Clinical Genetics Services)

Green List (high evidence)

13 affected individuals from 4 families reported (nonsense variants) with AD distal hereditary motor neuropathy. Variable penetrance was noted and phenotype severity differs greatly between patients. Functional studies show NMD and reduced protein levels in patient cells.
Created: 1 Mar 2021, 4:44 a.m. | Last Modified: 1 Mar 2021, 4:54 a.m.
Panel Version: 0.6494

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
hereditary motor neuropathy

Publications

Details

Mode of Inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Victorian Clinical Genetics Services
Phenotypes
  • Developmental and epileptic encephalopathy 5, MIM# 613477
  • Hereditary spastic paraplegia MONDO:0019064, SPTAN1-related
  • Neuronopathy, distal hereditary motor, 11, autosomal dominant, MIM# 620528
  • Autosomal dominant spastic paraplegia-91, with or without cerebellar ataxia (SPG91), MIM#620538
OMIM
182810
Clinvar variants
Variants in SPTAN1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

18 Oct 2023, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: SPTAN1 were changed from Developmental and epileptic encephalopathy 5, MIM# 613477; Hereditary spastic paraplegia MONDO:0019064, SPTAN1-related; Neuronopathy, distal hereditary motor, 11, autosomal dominant, MIM# 620528 to Developmental and epileptic encephalopathy 5, MIM# 613477; Hereditary spastic paraplegia MONDO:0019064, SPTAN1-related; Neuronopathy, distal hereditary motor, 11, autosomal dominant, MIM# 620528; Autosomal dominant spastic paraplegia-91, with or without cerebellar ataxia (SPG91), MIM#620538

1 Oct 2023, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: SPTAN1 were changed from Developmental and epileptic encephalopathy 5, MIM# 613477; Hereditary spastic paraplegia MONDO:0019064, SPTAN1-related; hereditary motor neuropathy to Developmental and epileptic encephalopathy 5, MIM# 613477; Hereditary spastic paraplegia MONDO:0019064, SPTAN1-related; Neuronopathy, distal hereditary motor, 11, autosomal dominant, MIM# 620528

28 Nov 2022, Gel status: 3

Set publications

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Publications for gene: SPTAN1 were set to 20493457; 22258530; 32811770; 33578420; 31332438

28 Nov 2022, Gel status: 3

Set mode of inheritance

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Mode of inheritance for gene: SPTAN1 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

30 May 2022, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: SPTAN1 were changed from Developmental and epileptic encephalopathy 5, MIM# 613477; hereditary motor neuropathy to Developmental and epileptic encephalopathy 5, MIM# 613477; Hereditary spastic paraplegia MONDO:0019064, SPTAN1-related; hereditary motor neuropathy

1 Mar 2021, Gel status: 3

Entity classified by Genomics England curator

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Gene: sptan1 has been classified as Green List (High Evidence).

1 Mar 2021, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: SPTAN1 were changed from to Developmental and epileptic encephalopathy 5, MIM# 613477; hereditary motor neuropathy

1 Mar 2021, Gel status: 3

Set publications

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Publications for gene: SPTAN1 were set to

1 Mar 2021, Gel status: 3

Set mode of inheritance

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Mode of inheritance for gene: SPTAN1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

1 Mar 2021, Gel status: 3

Set mode of inheritance

Alison Yeung (Victorian Clinical Genetics Services)

Mode of inheritance for gene: SPTAN1 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

17 Nov 2019, Gel status: 3

Created, Added New Source, Set mode of inheritance

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

gene: SPTAN1 was added gene: SPTAN1 was added to Mendeliome_VCGS. Sources: Expert Review Green,Victorian Clinical Genetics Services Mode of inheritance for gene: SPTAN1 was set to Unknown