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Intellectual disability

Gene: APTX

Red List (low evidence)

APTX (aprataxin)
EnsemblGeneIds (GRCh38): ENSG00000137074
EnsemblGeneIds (GRCh37): ENSG00000137074
OMIM: 606350, Gene2Phenotype
APTX is in 16 panels

5 reviews

Louise Daugherty (Genomics England Curator)

I don't know

Comment on list classification: Downgraded from Green to Red after internal clinical review. ID is not a clear feature. APTX variants cause ataxia and in some, cognitive decline. This is not a phenotype within the intended scope of the ID panel and is already green on the appropriate neurological panels.
Created: 8 Aug 2018, 11:36 a.m.
Due to a Red external review from external reviewer, and looking at the info again in the literature I am not sure why this gene was rated as Green based on the evidence, it is a confirmed G2P but is listed as a Mental deterioration/cognitive decline associated gene, this is not ID. Part of Movement disorder genes from BRIDGE. Past onto internal clinical team for further review and consideration to downgrade rating.
Created: 1 Aug 2018, 12:45 p.m.

Zornitza Stark (Australian Genomics)

Red List (low evidence)

Definitely a green gene but is it really intellectual disability? Seems more early-onset neurological deterioration and dementia.
Created: 14 Jun 2018, 8:56 a.m.

Caroline Wright (Sanger)

Green List (high evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
ATAXIA WITH OCULOMOTOR APRAXIA 1

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;in_omim_20150205_movement . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 5:05 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; gilissen_2014_known; omim_20150205_movement; Nijmegen_ID_diagnostic; Nijmegen_ID_candidates; 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, noon

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

Lu Raymond (university of cambridge )

Green List (high evidence)

History Filter Activity

8 Aug 2018, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: APTX were set to 11586300; 11586299; 15365154; 12196655; 15852392; 25529582; 24896178

8 Aug 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: aptx has been classified as Red List (Low Evidence).

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: 1

Set Mode of Inheritance, Added New Source

Ellen McDonagh (Genomics England Curator)

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

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

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