Intellectual disability - microarray and sequencing
Gene: ATL1
Please note additional recent publications. Principal association is with HSP/neuropathy phenotype, often of later onset. Few reports of intellectual disability as part of this condition (two families).Created: 14 Jun 2018, 9:24 a.m. | Last Modified: 17 Jul 2020, 12:03 a.m.
Panel Version: 3.175
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes
Neuropathy, hereditary sensory, type ID, MIM# 613708; Spastic paraplegia 3A, autosomal dominant, MIM# 182600
Publications
Variants in this GENE are reported as part of current diagnostic practice
The rating of this gene has been updated following NHS Genomic Medicine Service approval.Created: 9 Mar 2022, 3:40 p.m. | Last Modified: 9 Mar 2022, 3:40 p.m.
Panel Version: 3.1510
The "for-review" tag has been added to this gene as there is enough evidence for this gene to be rated RED at the next major review.Created: 16 Jul 2020, 4:28 p.m. | Last Modified: 16 Jul 2020, 4:28 p.m.
Panel Version: 3.175
Associated with phenotype in OMIM, not in G2P. Mental retardation has been reported in a second family (PMID 31236401). In this publication, the 9 year old proband and his maternal grandfather had hereditary spastic paraplegia and intellectual disability, however, proband's mother had hereditary spastic paraplegia, but no intelectual disability.Created: 16 Jul 2020, 4:24 p.m. | Last Modified: 16 Jul 2020, 4:24 p.m.
Panel Version: 3.175
Associated with phenotype in OMIM, not in G2P. Mild to severe late onset mental retardation in 10 members of a three generation family with Spastic paraplegia 3A, autosomal dominant 182600Created: 15 Dec 2017, 9:38 a.m. | Last Modified: 16 Jul 2020, 4:25 p.m.
Panel Version: 3.175
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications
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_omim_20150205_movement;in_movement_disorder_list;in_UKGTN_v12 . Main mutation mechanism : NACreated: 27 Jul 2017, 5:07 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : omim_20150205_movement; manju_list; UKGTN_v12; neuro_20160418_strict; NA. 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 TrustCreated: 19 Jul 2017, 12:02 p.m.
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications
Comment on list classification: Changed Red to Green from external expert review and further publications to support gene-disease associationCreated: 1 Aug 2018, 1:13 p.m.
Comment on list classification: Changed Red to Green from external expert review and further publications to support gene-disease associationCreated: 1 Aug 2018, 1:12 p.m.
Comment on phenotypes: added phenotypesCreated: 1 Aug 2018, 1:11 p.m.
Comment on publications: Added publications suggested from external reviewer to support gene-disease association, and upgrading of the gene to GreenCreated: 1 Aug 2018, 1:07 p.m.
Comment on mode of inheritance: updated MOI to not imprinted from external clinical reviewCreated: 1 Aug 2018, 1:06 p.m.
Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to access inclusion and pertinence to this panel.Created: 19 Jul 2017, 5:15 p.m.
Tag for-review was removed from gene: ATL1.
Source Expert Review Red was added to ATL1. Rating Changed from Green List (high evidence) to Red List (low evidence)
Tag for-review tag was added to gene: ATL1.
Publications for gene: ATL1 were set to 21336785; 28736820; 29180453; 29691679
Source Victorian Clinical Genetics Services was added to ATL1.
Gene: atl1 has been classified as Green List (High Evidence).
Gene: atl1 has been classified as Green List (High Evidence).
Phenotypes for gene: ATL1 were set to Spastic paraplegia 3A, autosomal dominant, 182600; Hereditary spastic paraplegia; Intellectual disability
Publications for gene: ATL1 were set to 21336785; 28736820; 29180453; 29691679
Mode of inheritance for gene: ATL1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
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.
Expert Review Red was added to ATL1. Panel: Intellectual disability Publications for gene ATL1 was set to ['21336785']
This gene has been classified as Amber List (Moderate Evidence).
ATL1 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene
ATL1 was created by BRIDGE