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Intellectual disability

Gene: NLGN4X

Red List (low evidence)

NLGN4X (neuroligin 4, X-linked)
EnsemblGeneIds (GRCh38): ENSG00000146938
EnsemblGeneIds (GRCh37): ENSG00000146938
OMIM: 300427, Gene2Phenotype
NLGN4X is in 3 panels

3 reviews

Olivia Niblock (Genomics England Curator)

Red List (low evidence)

From the literature (PMID: 14963808), a large extended family with several male members affected by intellectual disability and/or autism is described as having a two base pair deletion in this gene, resulting in a premature stop codon being produced. A founder effect mutation as all individuals are related and have the same mutation cannot be ruled out in this paper. Other papers (10922387, 19125102); describe patients with deletions including this gene among others, with intellectual disability ranging from mild to absent in 10922387 (no intellectual disability). In the other paper (19125102), an analysis was performed on children (all from a single population in Qinba mountains region of China) displaying Non Specific Mental Retardation (NSMR) and those with borderline IQ values for mental retardation, which displayed a possible link between NSMR and variants in the sixth exon of this gene. However, the details of the specific variants found in the sixth exon are not provided in the paper. The population is noted to be an isolated population with little in the way of infrastructure with a higher than average intellectual disability rate than is found in the general population, so a founder effect mutation cannot be ruled out here.

Additionally, PMID: 18194880 and 17391250 describe patients with deletions and variants in this gene with either no apparent phenotypic consequence on their IQs or a varied IQ range.

OMIM indicates that variants in this gene are linked to Autism Spectrum Disorder susceptibility, with three case study papers cited (PMID:12669065; 18231125; 10071191) and several non-case study papers (29428674; . Autism Spectrum Spectrum disorders without intellectual disability are not being included in the Intellectual Disability panel at this point in time.
Created: 7 Mar 2018, 11:48 a.m.

Publications

Caroline Wright (Sanger)

Red List (low evidence)

Mode of inheritance
X-LINKED: hemizygous mutation in males, biallelic mutations in females

Phenotypes
SUSCEPTIBILITY TO AUTISM X-LINKED TYPE 2 (AUTSX2)

Publications

  • 0

Lu Raymond (university of cambridge )

Red List (low evidence)

Details

Mode of Inheritance
X-LINKED: hemizygous mutation in males, biallelic mutations in females
Sources
  • Expert Review Red
  • Emory Genetics Laboratory
Phenotypes
  • SUSCEPTIBILITY TO AUTISM X-LINKED TYPE 2 (AUTSX2)
OMIM
300427
Clinvar variants
Variants in NLGN4X
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

29 Sep 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to NLGN4X.

12 Mar 2018, Gel status: 1

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.

12 Mar 2018, Gel status: 1

Set publications

Ellen McDonagh (Genomics England Curator)

Publications for gene NLGN4X was set to ['12669065', '18231125', '10071191', '29428674']

13 Nov 2015, Gel status: 1

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 1

Set Mode of Inheritance, Added New Source

Ellen McDonagh (Genomics England Curator)

NLGN4X was added to Intellectual disabilitypanel. Source: Expert Review Red Model of inheritance for gene NLGN4X was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

NLGN4X was added to Intellectual disabilitypanel. Sources: Emory Genetics Laboratory