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Intellectual disability

Gene: NR1I3

Red List (low evidence)
NR1I3 (nuclear receptor subfamily 1 group I member 3)
EnsemblGeneIds (GRCh38): ENSG00000143257
EnsemblGeneIds (GRCh37): ENSG00000143257
OMIM: 603881, Gene2Phenotype
NR1I3 is in 2 panels

3 reviews

Louise Daugherty (Genomics England Curator)

Red List (low evidence)

Comment on publications: added publications for the single de novo case and also supports inclusion of this gene on the ID panel, although currently there is not enough evidence to upgrade the rating
Created: 28 Feb 2018, 2:58 p.m.
From Koemans et al., 2017 (PMID: 29069077) Kleefstra syndrome, caused by haploinsufficiency of euchromatin histone methyltransferase 1 (EHMT1), is characterized by intellectual disability (ID), autism spectrum disorder (ASD), characteristic facial dysmorphisms, and other variable clinical features. In addition to EHMT1 mutations, de novo variants were reported in four additional genes (MBD5, SMARCB1, NR1I3, and KMT2C), in single individuals with clinical characteristics overlapping Kleefstra syndrome.
Created: 28 Feb 2018, 2:53 p.m.
This is a possible DD gene in Gene2Phenotype for EHMT1-LIKE INTELLECTUAL DISABILITY.
Created: 28 Feb 2018, 2:52 p.m.
In a girl with a syndromic form of mental retardation, Kleefstra et al., 2012 (PMID:22726846) identified a de novo heterozygous T-to-C transition at nucleotide 740 of the NR1I3 gene that resulted in a phe-to-ser substitution at codon 247 (F247S). They found a small number (4 cases) that were EHMT1 gene mutation-negative patients with core phenotypic features of Kleefstra syndrome but with phenotypic heterogeneity, referred to as Kleefstra syndrome spectrum (KSS), identifing de novo mutations in 4 genes, MBD5, MLL3, SMARCB, and NR1I3, that encode epigenetic regulators. Shared phenotypic features among these patients include intellectual disability and childhood hypotonia, present in all, and behavioral problems, synophrys, and midface hypoplasia, present in a majority. Otherwise the phenotypes were quite variable. Using Drosophila, Kleefstra et al. (2012) demonstrated that MBD5, MLL3, and NR1I3, cooperate with EHMT1; SMARCB1 was known to interact directly with MLL3.
Created: 28 Feb 2018, 2:46 p.m.
Comment on phenotypes: added phenotype from G2P
Created: 27 Feb 2018, 5:22 p.m.
Created: 27 Feb 2018, 5:22 p.m.

Panel version: Imported from Intellectual disability update Jan 2018 panel version 0.183

Caroline Wright (Sanger)

Red List (low evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
EHMT1-LIKE INTELLECTUAL DISABILITY

Publications

  • 0

Created: 5 Nov 2017, 2:42 a.m.

Panel version: 0

Lu Raymond (university of cambridge )

Red List (low evidence)

Created: 23 Feb 2016, 11:09 a.m.

Panel version: 0.306

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Red
Phenotypes
  • EHMT1-like Intellectual disability
OMIM
603881
Clinvar variants
Variants in NR1I3
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

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 NR1I3 was set to ['22726846', '29069077']

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: 0

Created

Ellen McDonagh (Genomics England Curator)

NR1I3 was created by ellenmcdonagh

13 Nov 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

NR1I3 was added to Intellectual disabilitypanel. Sources: Expert Review Red