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Intellectual disability

Gene: ATRX

Green List (high evidence)

ATRX (ATRX, chromatin remodeler)
EnsemblGeneIds (GRCh38): ENSG00000085224
EnsemblGeneIds (GRCh37): ENSG00000085224
OMIM: 300032, Gene2Phenotype
ATRX is in 15 panels

4 reviews

Rebecca Foulger (Genomics England curator)

Comment on mode of inheritance: Changed Mode of inheritance from XLR to XLD: Alpha-thalassemia/mental retardation syndrome, 301040 is listed as XLD in OMIM (in addition to Mental retardation-hypotonic facies syndrome, X-linked, 309580 listed as XLR). Although PMID:17503331 report that nearly all female carriers of ATRX syndrome have highly skewed X-chromosome inactivation in favour of cells expressing the normal ATRX allele and are essentially phenotypically normal, PMID:16955409 report a female carrier where the chromosome carrying the mutant allele was active and she therefore showed a phenotype.
Created: 22 Jul 2019, 8:21 a.m. | Last Modified: 22 Jul 2019, 8:21 a.m.
Panel Version: 2.959
PMID:16955409: Badens et al. 2006 report a 4 year old female with a heterozygous R246C variant in ATRX and a skewed pattern of X-inactivation where her maternally-inherited X chromosome that carried the de novo variant remained active. Clinical features included severed DD.
Created: 22 Jul 2019, 8:17 a.m. | Last Modified: 22 Jul 2019, 8:17 a.m.
Panel Version: 2.957
25606380: Moncini et al 2013 report 2 brothers with features including moderate ID and seizures. The ATRX c.109C>T (p.R37X) variant was present in both brothers, and the mother was a healthy carrier.
Created: 22 Jul 2019, 8:17 a.m. | Last Modified: 22 Jul 2019, 8:17 a.m.
Panel Version: 2.957

Caroline Wright (Sanger)

Green List (high evidence)

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

Phenotypes
MENTAL RETARDATION SYNDROMIC X-LINKED WITH HYPOTONIC FACIES SYNDROME TYPE 1 (MRXSHF1)

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_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_gilissen_2014_known . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 5:08 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; find_uk10k; gilissen_2014_known; sfari_20150206; Nijmegen_ID_diagnostic; Nijmegen_ID_candidates; gonzalez_mantilla_2016; GEL_ID_green_20160217; neuro_20160418_strict; Loss of function. 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, 12:03 p.m.

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

Publications

Lu Raymond (university of cambridge )

Green List (high evidence)

Details

Mode of Inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Sources
  • Victorian Clinical Genetics Services
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
  • Emory Genetics Laboratory
Phenotypes
  • Alpha-thalassemia/mental retardation syndrome, 301040
  • Mental retardation-hypotonic facies syndrome, X-linked, 309580
OMIM
300032
Clinvar variants
Variants in ATRX
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

22 Jul 2019, Gel status: 3

Set mode of inheritance

Rebecca Foulger (Genomics England curator)

Mode of inheritance for gene: ATRX was changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

22 Jul 2019, Gel status: 3

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: ATRX were set to 25529582; 24896178; 26860117; 26997013; 10995512; 7697714; 12116232; 15565397; 8644709; 9244431; 9598720

22 Jul 2019, Gel status: 3

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: ATRX were changed from Alpha-thalassemia/mental retardation syndrome, 301040Alpha-thalassemia myelodysplasia syndrome, somatic, 300448Mental retardation-hypotonic facies syndrome, X-linked, 309580; MENTAL RETARDATION SYNDROMIC X-LINKED WITH HYPOTONIC FACIES SYNDROME TYPE 1 (MRXSHF1) to Alpha-thalassemia/mental retardation syndrome, 301040; Mental retardation-hypotonic facies syndrome, X-linked, 309580

22 Jul 2019, Gel status: 3

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: ATRX were set to

28 Sep 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to ATRX.

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.

13 Nov 2015, Gel status: 4

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 4

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 2

Set Mode of Inheritance, Added New Source

Ellen McDonagh (Genomics England Curator)

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

24 Jun 2015, Gel status: 2

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene ATRX was changed to X-LINKED: hemizygous mutation in males, may be caused by monoallelic mutations in females

24 Jun 2015, Gel status: 2

Added New Source

Ellen McDonagh (Genomics England Curator)

ATRX was added to Intellectual disabilitypanel. Sources: Emory Genetics Laboratory,Radboud University Medical Center, Nijmegen

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

ATRX was added to Intellectual disabilitypanel. Sources: Emory Genetics Laboratory,Radboud University Medical Center, Nijmegen