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Intellectual disability
Gene: SHANK1

SHANK1 (SH3 and multiple ankyrin repeat domains 1)
EnsemblGeneIds (GRCh38): ENSG00000161681
EnsemblGeneIds (GRCh37): ENSG00000161681
OMIM: 604999, Gene2Phenotype
SHANK1 is in 3 panels

8 reviews

Eleanor Williams (Genomics England Curator)

This gene is not currently associated with a disease phenotype in OMIM, but checked PMID:34113010 to make sure it is the same gene listed in the publication as on this panel and it is, so added the gene-checked tag
Created: 16 Oct 2023, 8:11 p.m. | Last Modified: 16 Oct 2023, 8:11 p.m.

Panel Version: 5.313

Created: 16 Oct 2023, 8:11 p.m.
Last Modified: 16 Oct 2023, 8:11 p.m.
Panel version: 5.313

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to Green following NHS Genomic Medicine Service approval.
Created: 11 Oct 2023, 9:34 a.m. | Last Modified: 11 Oct 2023, 9:34 a.m.

Panel Version: 5.286

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Created: 11 Oct 2023, 9:34 a.m.
Last Modified: 11 Oct 2023, 9:34 a.m.
Panel version: 5.286

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There is sufficient evidence (at least four unrelated cases) for this gene to be promoted to GREEN at the next major review.
Created: 17 Apr 2023, 11:23 a.m. | Last Modified: 17 Apr 2023, 11:23 a.m.

Panel Version: 5.57

As reviewed by Zornitza Stark (Australian Genomics), PMID:34113010 reported six unrelated individuals who presented with neurodevelopmental disorders and identified with de novo truncating variants in SHANK1 gene. Of these six individuals, four had intellectual disability, one had severe learning difficulties and one with auditory processing disorder, difficulty with executive functioning, mathematic concepts, verbal reasoning and problem solving. Three of these patients were also reported with autism spectrum disorder.

This gene has been associated with relevant phenotypes in Gene2Phenotype (with 'strong' rating in the DD panel).
Created: 17 Apr 2023, 11:15 a.m. | Last Modified: 17 Apr 2023, 11:20 a.m.

Panel Version: 5.54

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071

Publications

34113010

Created: 17 Apr 2023, 11:06 a.m.
Last Modified: 17 Apr 2023, 11:20 a.m.
Panel version: 5.53

Zornitza Stark (Australian Genomics)

Green List (high evidence)

May et al. (2021) reported 6 individuals with developmental delay and autism with de novo truncating variants detected via WES. Evaluation of NMD resulted in stable transcripts, and the truncated SHANK1 completely lost binding with Homer1, a linker protein that binds to the C-terminus of SHANK1. Dispersed localization of the truncated SHANK1 variants within the spine and dendritic shaft was observed when expressed in neurons, indicating impaired synaptic localization of truncated SHANK1.

Also >10 individuals reported in autism cohorts +/- ID.
Created: 11 Oct 2021, 10 a.m. | Last Modified: 11 Oct 2021, 10 a.m.

Panel Version: 3.1338

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Neurodevelopmental disorder

Publications

Created: 11 Oct 2021, 10 a.m.
Last Modified: 11 Oct 2021, 10 a.m.
Panel version: 3.1338

Catherine Snow (Genomics England)

Red List (low evidence)

There is currently no evidence to suggest there is an association of this gene with intellectual disability. A number of papers with knockout mice implicate SHANK1 plays a role in learning and cognition but no evidence in humans.
Created: 5 Aug 2019, 10:14 a.m. | Last Modified: 5 Aug 2019, 10:14 a.m.

Panel Version: 2.993

Publications

Created: 5 Aug 2019, 10:14 a.m.
Last Modified: 5 Aug 2019, 10:14 a.m.
Panel version: 2.993

Chris Buxton (North Bristol NHS Trust)

This gene has no OMIM disorder listed against it. There are 2 'Green' reviews listed against this gene for ID panel, but with no supporting evidence - what is the evidence for its inclusion as a Green gene?
Created: 23 Jul 2019, 12:53 p.m. | Last Modified: 23 Jul 2019, 12:53 p.m.

Panel Version: 2.967

Created: 23 Jul 2019, 12:53 p.m.
Last Modified: 23 Jul 2019, 12:53 p.m.
Panel version: 2.967

Caroline Wright (Sanger)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
AUTISM

Publications

Created: 5 Nov 2017, 2:42 a.m.

Panel version: 0

Lu Raymond (university of cambridge )

Green List (high evidence)

Created: 23 Feb 2016, 10:52 a.m.

Panel version: 0.306

Details

Mode of Inheritance

MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Sources

Expert Review Green
NHS GMS

Phenotypes

neurodevelopmental disorder, MONDO:0700092
intellectual disability, MONDO:0001071

Tags

gene-checked

OMIM

604999

Clinvar variants

Variants in SHANK1

Penetrance

Complete

Publications

34113010

Panels with this gene

History Filter Activity

16 Oct 2023, Gel status: 3

Added Tag

Eleanor Williams (Genomics England Curator)

Tag gene-checked tag was added to gene: SHANK1.

11 Oct 2023, Gel status: 3

Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag Q2_23_promote_green was removed from gene: SHANK1.

11 Oct 2023, Gel status: 3

Added New Source, Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source NHS GMS was added to SHANK1. Source Expert Review Green was added to SHANK1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

17 Apr 2023, Gel status: 2