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Intellectual disability

Gene: SNIP1

Amber List (moderate evidence)

SNIP1 (Smad nuclear interacting protein 1)
EnsemblGeneIds (GRCh38): ENSG00000163877
EnsemblGeneIds (GRCh37): ENSG00000163877
OMIM: 608241, Gene2Phenotype
SNIP1 is in 3 panels

4 reviews

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with relevant phenotype in OMIM and as possible Gen2Phen gene. A single (founder) variant NM_024700.4:c.1097A>G, p.(Glu366Gly) has been reported in over 30 cases of Psychomotor retardation, epilepsy, and craniofacial dysmorphism OMIM:614501 in the Amish community (PMIDs: 22279524; 34570759). Cases are homozygous for this variant and unaffected members of the families are heterozygous or wt. Overexpression of the equivalent mouse variant in mouse inner medullary collecting duct cells, resulted in a more aggregated appearance in the nucleus compared to wildtype. The variant protein maybe unstable as Western blots showed reduced levels of the variant protein (PMID: 22279524). Whole transcriptomic analysis of patient blood was performed in PMID: 34570759. This revealed 11 upregulated and 32 downregulated genes, of which 24 had previously been associated with neurological disease.
Created: 12 Oct 2021, 5:14 p.m. | Last Modified: 12 Oct 2021, 5:14 p.m.
Panel Version: 3.1352

Caroline Wright (Sanger)

Red List (low evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
SYMPTOMATIC EPILEPSY AND SKULL DYSPLASIA

Publications

Rebecca Foulger (Genomics England curator)

Red List (low evidence)

ID link but insufficient unrelated cases to rate Green: 3 Amish patients with severe developmental delay reported in PMID:22279524 (2012) with 1097A-G, p.E366G variant in SNIP1.
Created: 31 Oct 2017, 9:24 a.m.

Phenotypes
Psychomotor retardation, epilepsy, and craniofacial dysmorphism, 614501; severe developmental delay

Publications

Lu Raymond (university of cambridge )

Red List (low evidence)

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Victorian Clinical Genetics Services
Phenotypes
  • Psychomotor retardation, epilepsy, and craniofacial dysmorphism OMIM:614501
  • psychomotor retardation, epilepsy, and craniofacial dysmorphism MONDO:0013787
Tags
founder-effect
OMIM
608241
Clinvar variants
Variants in SNIP1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

12 Oct 2021, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: snip1 has been classified as Amber List (Moderate Evidence).

12 Oct 2021, Gel status: 1

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: SNIP1 were set to 22279524

12 Oct 2021, Gel status: 1

Added Tag

Sarah Leigh (Genomics England Curator)

Tag founder-effect tag was added to gene: SNIP1.

12 Oct 2021, Gel status: 1

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: SNIP1 were changed from Psychomotor retardation, epilepsy, and craniofacial dysmorphism, 614501; severe developmental delay to Psychomotor retardation, epilepsy, and craniofacial dysmorphism OMIM:614501; psychomotor retardation, epilepsy, and craniofacial dysmorphism MONDO:0013787

29 Sep 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to SNIP1.

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.

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)

SNIP1 was added to Intellectual disabilitypanel. Sources: Expert Review Red

13 Nov 2015, Gel status: 0

Created

Ellen McDonagh (Genomics England Curator)

SNIP1 was created by ellenmcdonagh