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Intellectual disability

Gene: SCN4A

Amber List (moderate evidence)

SCN4A (sodium voltage-gated channel alpha subunit 4)
EnsemblGeneIds (GRCh38): ENSG00000007314
EnsemblGeneIds (GRCh37): ENSG00000007314
OMIM: 603967, Gene2Phenotype
SCN4A is in 15 panels

4 reviews

Zornitza Stark (Australian Genomics)

Red List (low evidence)

ID is not part of the phenotype.
Created: 7 Feb 2020, 7:48 a.m. | Last Modified: 7 Feb 2020, 7:48 a.m.
Panel Version: 3.0

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Phenotypes
Hyperkalemic periodic paralysis, type 2, MIM# 170500; Hypokalemic periodic paralysis, type 2, MIM# 613345; Myasthenic syndrome, congenital, 16, MIM# 614198; Myotonia congenita, atypical, acetazolamide-responsive 608390; Paramyotonia congenita 168300

Andrea Haworth (ACGS, Congenica)

Please can you clarify the evidence that variants in SCN4A are associated with intellectual disability-I am struggling to find published resources outside it's involvement in neuromuscular disorders.
Created: 30 Jan 2020, 4:41 p.m. | Last Modified: 30 Jan 2020, 4:41 p.m.
Panel Version: 3.0

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf;in_UKGTN_v12 . Main mutation mechanism : Activating; All missense/in frame
Created: 27 Jul 2017, 8:20 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; UKGTN_v12; neuro_20160418_strict; Activating; All missense/in frame. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 1:19 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Publications

Mode of pathogenicity

Louise Daugherty (Genomics England Curator)

Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to assess inclusion and pertinence to this panel.
Created: 20 Jul 2017, 1:48 p.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Amber
Phenotypes
  • Hyperkalemic periodic paralysis, type 2, 170500
  • Paramyotonia
  • congenita, 168300
  • Myotonia congenita, atypical, acetazolamide-responsive, 608390
  • Myasthenic syndrome, acetazolamide-responsive, 614198
  • Hypokalemic periodic paralysis, type 2, 613345
OMIM
603967
Clinvar variants
Variants in SCN4A
Penetrance
Complete
Mode of Pathogenicity
Other - please provide details in the comments
Panels with this gene

History Filter Activity

12 Mar 2018, Gel status: 2

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

20 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

19 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

SCN4A was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

SCN4A was created by BRIDGE