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Intellectual disability

Gene: NT5C2

Green List (high evidence)

NT5C2 (5'-nucleotidase, cytosolic II)
EnsemblGeneIds (GRCh38): ENSG00000076685
EnsemblGeneIds (GRCh37): ENSG00000076685
OMIM: 600417, Gene2Phenotype
NT5C2 is in 6 panels

3 reviews

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Sufficient cases; variable as to whether spasticity is the main presenting feature or global delay, but as both are reported it would be appropriate for inclusion on this panel on phenotypic grounds.
Created: 5 Mar 2018, 12:33 p.m.

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 . Main mutation mechanism : NA
Created: 27 Jul 2017, 7:52 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : omim_20150205_movement; manju_list; 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, 12:58 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

  • omim.org
  • Personal communication with NIHRBRRD BRIDGE SPEED

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

Comment on list classification: Promoted gene status from Amber to Green due to evidence found in more than three individuals for ID phenotype.Comment on publications: added publications to support the Intellectual Disability phenotype observed in Spastic paraplegia 45, autosomal recessive with ID phenotype. Comment on phenotypes: Added phenotype from OMIM and from PMID: 19415352, 24482476. Although predominately the variants cause a movement disorder phenotype, intellectual Disability is a feature, and has been reported in 5 unrelated families. Novarino et al. (2014) PMID: 24482476 reported 4 of the five families had ID phenotype (6 affecteds) and Dursun et al. (2009) PMID:19415352 reported a consanguineous Turkish family in which 5 individuals had a form of complicated spastic paraplegia with mental retardation.
Created: 12 Mar 2018, 9:47 a.m.
Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to assess inclusion and pertinence to this panel.
Created: 20 Jul 2017, 1 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Spastic paraplegia 45, autosomal recessive, 613162; Intellectual disability

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Spastic paraplegia 45, autosomal recessive, 613162
  • Intellectual disability
OMIM
600417
Clinvar variants
Variants in NT5C2
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

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.

12 Mar 2018, Gel status: 3

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

12 Mar 2018, Gel status: 4

Added New Source, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Green was added to NT5C2. Panel: Intellectual disability Publications for gene NT5C2 was set to ['20301682', '24482476', '19415352']

20 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)

NT5C2 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

NT5C2 was created by BRIDGE