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Intellectual disability

Gene: ALX4

Amber List (moderate evidence)

ALX4 (ALX homeobox 4)
EnsemblGeneIds (GRCh38): ENSG00000052850
EnsemblGeneIds (GRCh37): ENSG00000052850
OMIM: 605420, Gene2Phenotype
ALX4 is in 6 panels

7 reviews

Louise Daugherty (Genomics England Curator)

I don't know

In view of external Green review and after internal review it was decided to keep this gene Amber on the ID panel, as it does not seem to be a consistently predominant feature. ALX4 is noted as having significant findings wrt PMID 29215649 but phenotypically supports inclusion on the craniosynostosis panel, where this gene is rated as Green
Created: 12 Sep 2018, 4:27 p.m.
Comment on mode of inheritance: changed MOI to both;Parietal foramina 2, (AD), 609597;Frontonasal dysplasia 2, (AR), 613451
Created: 13 Aug 2018, 4:59 p.m.
Comment on publications: Added publications suggested from external expert review to support upgrading of the gene to Green
Created: 13 Aug 2018, 4:40 p.m.
Due to a Green review from external clinical reviewer, this gene was reviewed again in view of additional publications, there are enough cases to support the gene being rating as Green, although noted by external review intellectual disabilities not always present/variable so passed onto clinical team for further review.
Created: 13 Aug 2018, 4:13 p.m.
Comment on publications: Added publications suggested by external review to support gene-disease association, and upgrading of the gene to Green
Created: 13 Aug 2018, 3:43 p.m.

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Two more recent publications; agree intellectual disability not always present/variable.
Created: 14 Jun 2018, 8:42 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

Variants in this GENE are reported as part of current diagnostic practice

Ellen McDonagh (Genomics England Curator)

Comment when marking as ready: Updated based on the latest reviews displayed here from the Intellectual disability update Oct 2017 panel.
Created: 29 Nov 2017, 3:55 p.m.

Caroline Wright (Sanger)

Red List (low evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
PARIETAL FORAMINA 2

Sarah Leigh (Genomics England Curator)

I don't know

Associated with phenotype in OMIM and as a confirmed G2P. At least three variants reported, however, not all cases display intellectual disabilities
Created: 31 Oct 2017, 9:57 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Frontonasal dysplasia 2 613451

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_UKGTN_v12 . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 5:04 p.m.

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Publications

Lu Raymond (university of cambridge )

Red List (low evidence)

Details

Mode of Inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Parietal foramina
  • Parietal foramina 2, (AD), 609597
  • Frontonasal dysplasia 2, (AR), 613451
OMIM
605420
Clinvar variants
Variants in ALX4
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

28 Sep 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to ALX4.

13 Aug 2018, Gel status: 2

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: ALX4 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

13 Aug 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: ALX4 were set to Parietal foramina; Parietal foramina 2, (AD), 609597; Frontonasal dysplasia 2, (AR), 613451

13 Aug 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: ALX4 were set to Frontonasal dysplasia 2, 613451; Parietal foramina; Parietal foramina 2, (AD), 609597

13 Aug 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: ALX4 were set to Frontonasal dysplasia 2, 613451 Parietal foramina; Parietal foramina 2, (AD), 609597

13 Aug 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: ALX4 were set to 22140057; 24668755; 25529582; 29681084; 29215649

13 Aug 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: ALX4 were set to Frontonasal dysplasia 2, 613451

13 Aug 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: ALX4 were set to 22140057; 24668755; 25529582

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.

29 Nov 2017, Gel status: 2

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

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

29 Nov 2017, Gel status: 2

Set publications

Ellen McDonagh (Genomics England Curator)

Publications for ALX4 were set to 22140057; 24668755; 25529582

29 Nov 2017, Gel status: 2

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

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

29 Nov 2017, Gel status: 2

Added New Source, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Amber was added to ALX4. Panel: Intellectual disability Publications for gene ALX4 was set to ['22140057', ' 24668755']

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)

ALX4 was added to Intellectual disabilitypanel. Source: Expert Review Red Model of inheritance for gene ALX4 was set to BIALLELIC, autosomal or pseudoautosomal

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

ALX4 was added to Intellectual disabilitypanel. Sources: Radboud University Medical Center, Nijmegen