Early onset or syndromic epilepsy
Gene: SPTAN1EnsemblGeneIds (GRCh38): ENSG00000197694
EnsemblGeneIds (GRCh37): ENSG00000197694
OMIM: 182810, Gene2Phenotype
SPTAN1 is in 10 panels
7 reviews
Arina Puzriakova (Genomics England Curator)
Comment on phenotypes: OMIM phenotypes accessed on 16-02-2026Created: 16 Feb 2026, 2:20 p.m. | Last Modified: 16 Feb 2026, 2:20 p.m.
Panel Version: 8.112
Rebecca Foulger (Genomics England curator)
Review and rating collated by Tracy Lester (Oxford Medical Genetics Laboratories Oxford University Hospitals NHS Foundation Trust, 2019_02_06) on behalf of Wessex and West Midlands GLH for GMS Neurology specialist test group, for Clinical Indication R59 'Early onset or syndromic epilepsy'. Review contributors: John Taylor and Helen Lord. Suggested gene rating: Green.Created: 6 Aug 2019, 8:38 p.m. | Last Modified: 6 Aug 2019, 8:38 p.m.
Panel Version: 1.189
Tracy Lester (Genetics laboratory, Oxford UK)
AD EIEE. OMIM Tohyama et al, 2008 & Saitsu et al, 2010 - 2 unrelated Japenese patients with EIEE - de novo het variants - in vitro functional studies suggest dom-neg effect. Hamdan et al, 2012 - de novhet variant in a boy with EIEE. HGMD Pro - more variants listed - Syrbe et al, 2017 - 20 patients with pathoenic/likely pathogenic SPTAN1 variants. 16 de novo (7 unique missense and 9 in frame del/dups - recurrent 3AA dup in 5 patients). 14 patients had epilepsy.Created: 6 Aug 2019, 8:31 p.m. | Last Modified: 6 Aug 2019, 8:31 p.m.
Panel Version: 1.188
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes
Epileptic encephalopathy, early infantile, 613477
Publications
Amy McTague (UCL Institute of Child Health)
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes
Epileptic encephalopathy, early infantile, 5
Publications
- Saitsu et al (2010) Am J Hum Genet 86: 881_891
Variants in this GENE are reported as part of current diagnostic practice
Natalie Trump (NHS - Great Ormond Street Hospital)
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes
Epileptic encephalopathy, early infantile, 5
Publications
- Saitsu et al (2010) Am J Hum Genet 86: 881_891
Variants in this GENE are reported as part of current diagnostic practice
Manju Kurian (UCL-Institute of Child Health)
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes
Epileptic encephalopathy, early infantile, 5
Publications
- Saitsu et al (2010) Am J Hum Genet 86: 881_891
Variants in this GENE are reported as part of current diagnostic practice
Richard Scott (North Thames GMC/UCL)
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes
Epileptic encephalopathy, early infantile, 5
Publications
- Saitsu et al (2010) Am J Hum Genet 86: 881 891
Mode of pathogenicity
loss-of-function (truncating variants and curated list of variants)
Variants in this GENE are reported as part of current diagnostic practice
Details
- Mode of Inheritance
- MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
- Sources
-
- Wessex and West Midlands GLH
- NHS GMS
- NIHRBR-RD Consortium SPEED_v3.0_20170404
- Victorian Clinical Genetics Services
- Illumina TruGenome Clinical Sequencing Services
- Radboud University Medical Center, Nijmegen
- UKGTN
- Expert
- Expert Review Green
- Phenotypes
-
- Developmental and epileptic encephalopathy 5, OMIM:613477
- Developmental delay with or without epilepsy, OMIM:620540
- Spastic paraplegia 91, autosomal dominant, with or without cerebellar ataxia, OMIM:620538
- OMIM
- 182810
- Clinvar variants
- Variants in SPTAN1
- Penetrance
- None
- Publications
- Panels with this gene
-
- Hereditary neuropathy or pain disorder
- Hereditary ataxia with onset in adulthood
- Early onset or syndromic epilepsy
- Adult onset hereditary spastic paraplegia
- Intellectual disability
- Fetal anomalies
- Distal myopathies
- DDG2P
- Ataxia and cerebellar anomalies - narrow panel
- Childhood onset hereditary spastic paraplegia
History Filter Activity
Set Phenotypes
Arina Puzriakova (Genomics England Curator)Phenotypes for gene: SPTAN1 were changed from Developmental and epileptic encephalopathy 5, OMIM:613477; developmental and epileptic encephalopathy, 5, MONDO:0013277 to Developmental and epileptic encephalopathy 5, OMIM:613477; Developmental delay with or without epilepsy, OMIM:620540; Spastic paraplegia 91, autosomal dominant, with or without cerebellar ataxia, OMIM:620538
Set Phenotypes
Sarah Leigh (Genomics England Curator)Phenotypes for gene: SPTAN1 were changed from Epileptic encephalopathy, early infantile, 5 to Developmental and epileptic encephalopathy 5, OMIM:613477; developmental and epileptic encephalopathy, 5, MONDO:0013277
Set publications
Sarah Leigh (Genomics England Curator)Publications for gene: SPTAN1 were set to Saitsu et al (2010) Am J Hum Genet 86: 881_891
Added New Source
Rebecca Foulger (Genomics England curator)Source Wessex and West Midlands GLH was added to SPTAN1.
Added New Source
Rebecca Foulger (Genomics England curator)Source NHS GMS was added to SPTAN1.
Panel promoted to version 1.0
Sarah Leigh (Genomics England Curator)Ellen McDonagh: Comment on mode of inheritance
Added New Source
Sarah Leigh (Genomics England Curator)NIHRBR-RD Consortium SPEED_v3.0_20170404 was added to SPTAN1. Panel: Genetic Epilepsy Syndromes
Added New Source
Sarah Leigh (Genomics England Curator)Victorian Clinical Genetics Services was added to SPTAN1. Panel: Genetic Epilepsy Syndromes
Added New Source
Sarah Leigh (Genomics England Curator)SPTAN1 was added to Genetic Epilepsy Syndromes panel. Sources: Expert Review Green,Expert,UKGTN,Radboud University Medical Center, Nijmegen,Illumina TruGenome Clinical Sequencing Services
Created
Sarah Leigh (Genomics England Curator)SPTAN1 was created by Sarah Leigh