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Intellectual disability

Gene: NFIA

Green List (high evidence)

NFIA (nuclear factor I A)
EnsemblGeneIds (GRCh38): ENSG00000162599
EnsemblGeneIds (GRCh37): ENSG00000162599
OMIM: 600727, Gene2Phenotype
NFIA is in 4 panels

4 reviews

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Three unrelated cases with variants / deletions involving this gene and a relevant phenotype.
Created: 8 Mar 2018, 3:22 p.m.
Comment on list classification: Three unrelated cases with NFIA variants (1 frameshifting SNV and 2 intragenic deletions; involving exons 4-9 and exons 1-2). Phenotypes reported include delayed psychomotor development / developmental delay, in association with other features (mainly renal). On balance this reaches the threshold for inclusion and supports a LOF mechanism.
Created: 8 Mar 2018, 3:22 p.m.

Louise Daugherty (Genomics England Curator)

Comment on list classification: Three unrelated cases in the literature to specifically support NFIA causing Brain malformations with or without urinary tract defects (ID being part of the clinical phenotype).
Created: 5 Mar 2018, 5:43 p.m.
Comment on phenotypes: Associated to CHROMOSOME 1P32-P31 DELETION SYNDROME, INCLUDED Weining Lu et al., (2007) PMID: 17530927.
Created: 5 Mar 2018, 5:34 p.m.
Although the publications referenced are all for the single gene NFIA causing Brain malformations with or without urinary tract defects some patients with a similar phenotype have larger deletions of chromosome 1p32-p31, including the NFIA gene; this disorder thus represents a contiguous gene deletion syndrome.
Created: 5 Mar 2018, 5:30 p.m.
added tag deletions. Currently only pathogenic deletion variants are reported for this gene.
Created: 5 Mar 2018, 5:16 p.m.
Comment on publications: Rao et al. (2014) PMID: 24462883 identified a de novo heterozygous 120-kb intragenic deletion for BRMUTD . Negishi et al. (2015) PMID: 27081522 identified a de novo heterozygous 1-bp deletion (c.1094delC, NM_001134673.3) in the NFIA gene, resulting in a frameshift and premature termination (Pro365HisfsTer32)
and Nyboe et al. (2015) 25714559- in a family (4 affecteds) they identified heterozygosity for a 109-kb intragenic deletion (chr1.61,497,698-61,607,171, GRCh37) that affected exons 1 and 2 of the NFIA gene
Created: 5 Mar 2018, 5:15 p.m.

Caroline Wright (Sanger)

Red List (low evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
CHROMOSOME 1P32-P31 DELETION SYNDROME

Publications

Lu Raymond (university of cambridge )

Red List (low evidence)

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
  • Expert Review Red
Phenotypes
  • Brain malformations with or without urinary tract defects, 613735
  • BRMUTD
  • Intellectual disability
  • Chromosome 1p32-p31 deletion syndrome, included
Tags
deletions
OMIM
600727
Clinvar variants
Variants in NFIA
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

12 Mar 2018, Gel status: 4

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: 4

Added New Source, Set mode of inheritance, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Green was added to NFIA. Panel: Intellectual disability Model of inheritance for gene NFIA was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene NFIA was set to ['24462883', '27081522', '25714559', '22031302', '17530927']

13 Nov 2015, Gel status: 1

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

NFIA was added to Intellectual disabilitypanel. Sources: Expert Review Red

13 Nov 2015, Gel status: 0

Created

Ellen McDonagh (Genomics England Curator)

NFIA was created by ellenmcdonagh