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Intellectual disability

Gene: ATL1

Green List (high evidence)

ATL1 (atlastin GTPase 1)
EnsemblGeneIds (GRCh38): ENSG00000198513
EnsemblGeneIds (GRCh37): ENSG00000198513
OMIM: 606439, Gene2Phenotype
ATL1 is in 11 panels

4 reviews

Zornitza Stark (Australian Genomics)

Red List (low evidence)

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

Sarah Leigh (Genomics England Curator)

Red List (low evidence)

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 182600
Created: 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

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_omim_20150205_movement;in_movement_disorder_list;in_UKGTN_v12 . Main mutation mechanism : NA
Created: 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 Trust
Created: 19 Jul 2017, 12:02 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Publications

  • omim.org
  • Personal communication with NIHRBRRD BRIDGE SPEED
  • Version 12 ukgtn.nhs.uk

Louise Daugherty (Genomics England Curator)

Comment on list classification: Changed Red to Green from external expert review and further publications to support gene-disease association
Created: 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 association
Created: 1 Aug 2018, 1:12 p.m.
Comment on phenotypes: added phenotypes
Created: 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 Green
Created: 1 Aug 2018, 1:07 p.m.
Comment on mode of inheritance: updated MOI to not imprinted from external clinical review
Created: 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.

Details

History Filter Activity

16 Jul 2020, Gel status: 3

Added Tag

Sarah Leigh (Genomics England Curator)

Tag for-review tag was added to gene: ATL1.

16 Jul 2020, Gel status: 3

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: ATL1 were set to 21336785; 28736820; 29180453; 29691679

28 Sep 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to ATL1.

1 Aug 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: atl1 has been classified as Green List (High Evidence).

1 Aug 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: atl1 has been classified as Green List (High Evidence).

1 Aug 2018, Gel status: 1

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: ATL1 were set to Spastic paraplegia 3A, autosomal dominant, 182600; Hereditary spastic paraplegia; Intellectual disability

1 Aug 2018, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: ATL1 were set to 21336785; 28736820; 29180453; 29691679

1 Aug 2018, Gel status: 1

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: ATL1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

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.

5 Jan 2018, Gel status: 1

Added New Source, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Red was added to ATL1. Panel: Intellectual disability Publications for gene ATL1 was set to ['21336785']

19 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

19 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

ATL1 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

ATL1 was created by BRIDGE