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Intellectual disability

Gene: LGI4

Green List (high evidence)

LGI4 (leucine rich repeat LGI family member 4)
EnsemblGeneIds (GRCh38): ENSG00000153902
EnsemblGeneIds (GRCh37): ENSG00000153902
OMIM: 608303, Gene2Phenotype
LGI4 is in 6 panels

2 reviews

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

Comment on phenotypes: added phenotypes to support inclusion on ID panel
Created: 23 Feb 2018, 2:55 p.m.
New gene/phenotype relationship(s) cataloged in OMIM. AMCNMY is severe neurologic disorder with onset in utero. Most affected individuals die in utero, subject to pregnancy termination because of lack of fetal movements and prenatal evidence of contractures of virtually all joints or die in the neonatal period. Those who survive have generalized contractures and hypotonia. The disorder is caused by a neurogenic defect and poor or absent myelin formation around peripheral nerves rather than by a muscular defect, Xue et al., 2017 PMID: 28318499. Evidence in 9 offspring from 4 unrelated families, combined with evidence from expert list (BRIDGE), the gene can be promoted to Green rating. Listed in Decipher v9.17 some cases with Intellectual disability and global developmental delay.
Created: 17 Aug 2017, 2:05 p.m.
Comment on list classification: Changed from Amber to Green due to evidence in the literature (OMIM update) and from expert list BRIDGE project SPEED project (Specialist Pathology: Evaluating Exomes in Diagnostics project)
Created: 17 Aug 2017, 1:36 p.m.
Comment on phenotypes: addedMIM
Created: 17 Aug 2017, 12:56 p.m.
Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to access inclusion and pertinence to this panel.
Created: 28 Jul 2017, 1:03 p.m.

Publications

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_manual . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 7:14 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

  • Manual assessment of Genes of interest from literature searches and personal communication

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Arthrogryposis Multiplex Congenita
  • Arthrogryposis multiplex congenita, neurogenic, with myelin defect, 617468
  • AMCNMY
  • Intellectual disability
  • Global developmental delay
OMIM
608303
Clinvar variants
Variants in LGI4
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

12 Mar 2018, Gel status: 3

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.

23 Feb 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for LGI4 were set to Arthrogryposis Multiplex Congenita; Arthrogryposis multiplex congenita, neurogenic, with myelin defect, 617468; AMCNMY; Intellectual disability; Global developmental delay

23 Feb 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for LGI4 were set to Arthrogryposis Multiplex Congenita; Arthrogryposis multiplex congenita, neurogenic, with myelin defect, 617468; AMCNMY; Intellectual disability; Global developmental delay

17 Aug 2017, Gel status: 4

Set publications

Louise Daugherty (Genomics England Curator)

Publications for LGI4 were set to 28318499; 15857855; 16341215

17 Aug 2017, Gel status: 4

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

17 Aug 2017, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for LGI4 were set to Arthrogryposis Multiplex Congenita; Arthrogryposis multiplex congenita, neurogenic, with myelin defect, 617468;AMCNMY

17 Aug 2017, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for LGI4 were set to Arthrogryposis Multiplex Congenita; Arthrogryposis multiplex congenita, neurogenic, with myelin defect, 617468

28 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).

27 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

LGI4 was created by BRIDGE

27 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

LGI4 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene