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Intellectual disability

Gene: NIPA1

Red List (low evidence)

NIPA1 (non imprinted in Prader-Willi/Angelman syndrome 1)
EnsemblGeneIds (GRCh38): ENSG00000170113
EnsemblGeneIds (GRCh37): ENSG00000170113
OMIM: 608145, Gene2Phenotype
NIPA1 is in 9 panels

2 reviews

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, 7:48 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : omim_20150205_movement; sfari_20150206; 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, 12:57 p.m.

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

Publications

  • omim.org
  • Personal communication with NIHRBRRD BRIDGE SPEED

Louise Daugherty (Genomics England Curator)

Red List (low evidence)

Comment on phenotypes: added phenotype from OMIM and Orphanet. Comment on publications: added publications to support Spastic paraplegia 6 phenotype. Comment on list classification: Changed gene from status Amber to Red, the variants of NIPA1 cause a movement disorder phenotype, intellectual disability is not a feature. Gene on ID panel possibility due to ID being associated to duplications or micordeletions in particular region is characterized by low mental retardation, autism, developmental delay. PMID: 27577220, 24123946. Internal clinical review confirmed Red status for this gene on this panel. It was noted that although NIPA1 is commonly deleted in a recurrent neuro-susceptibility locus, we do not have evidence for causation for it alone.
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, 1:01 p.m.

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

Phenotypes
Spastic paraplegia 6, autosomal dominant, 600363; Non Imprinted In Prader-Willi, Angelman Syndrome 1

Publications

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Amber
Phenotypes
  • Spastic paraplegia 6, autosomal dominant, 600363
  • Non Imprinted In Prader-Willi/Angelman Syndrome 1
OMIM
608145
Clinvar variants
Variants in NIPA1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

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.

12 Mar 2018, Gel status: 1

Added New Source, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Red was added to NIPA1. Panel: Intellectual disability Publications for gene NIPA1 was set to ['14508710', '15643603', '15711826']

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)

NIPA1 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

NIPA1 was created by BRIDGE