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Intellectual disability

Gene: SALL1

Amber List (moderate evidence)

SALL1 (spalt like transcription factor 1)
EnsemblGeneIds (GRCh38): ENSG00000103449
EnsemblGeneIds (GRCh37): ENSG00000103449
OMIM: 602218, Gene2Phenotype
SALL1 is in 17 panels

5 reviews

Helen Brittain (Genomics England Curator)

Comment when marking as ready: As per Louise Daugherty's review; ID is noted in 5-10% of people with Townes-Brocks syndrome. However the majority of these are in the mild end of the spectrum. Although the ID panel is intended to be inclusive, the severity of ID in those recruited is intended to be at least of moderate severity. On reflection, an amber rating may be more appropriate.
Created: 21 Dec 2017, 2:26 p.m.
Comment on list classification: As per Louise Daugherty's review; ID is noted in 5-10% of people with Townes-Brocks syndrome. However the majority of these are in the mild end of the spectrum. Although the ID panel is intended to be inclusive, the severity of ID in those recruited is intended to be at least of moderate severity. On reflection, an amber rating may be more appropriate.
Created: 21 Dec 2017, 2:25 p.m.

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

ID is not be reported as a manifestation of TBS, as most patients with TBS described in the literature have been reported to be of normal intelligence, however mild or moderate mental retardation occurs in approximately 10% of cases, a 3 to 4 fold the rate of mental retardation in the general population (PMID:6741990). This is a confirmed gene in Developmental Disorders Genotype-Phenotype Database (DDG2P). There are a number of unrelated cases where ID is part of the observed clinical phenotype. PMID: 29110636 (2017) describes a 5-year-old Brazilian boy exhibiting developmental and speech delays, PMID: 27277004 (2016) describes a girl with IQ in the seventies, processing problems, and a sensory integration disorder, PMID 1951448 (1991) reported 2 unrelated children with mental retardation that was not related to hearing loss (described as mild). Discussed with clinical team who agree that ID is a relatively infrequent feature, however, higher than the population rate in the cohort so on balance thought it was worth including given the inclusive aim of the ID panel.
Created: 5 Jan 2018, 2:42 p.m.
Comment on phenotypes: format amendment
Created: 29 Nov 2017, 3:22 p.m.

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

Phenotypes
Townes-Brocks branchiootorenal-like syndrome, 107480; Townes-Brocks syndrome 1, 107480; TBS

Publications

Caroline Wright (Sanger)

Red List (low evidence)

Phenotypes
TOWNES-BROCKS SYNDROME (TBS)

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_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf;in_gilissen_2014_known;in_UKGTN_v12 . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 8:19 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; gilissen_2014_known; UKGTN_v12; Nijmegen_ID_diagnostic; Nijmegen_ID_candidates; GEL_ID_red_20160217; neuro_20160418_strict; Loss of function. 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, 1:18 p.m.

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

Publications

Lu Raymond (university of cambridge )

Red List (low evidence)

History Filter Activity

12 Mar 2018, Gel status: 2

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.

5 Jan 2018, Gel status: 2

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

5 Jan 2018, Gel status: 1

Set mode of inheritance, Set publications

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SALL1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene SALL1 was set to ['6741990', ' 29110636', '27277004', '1951448', '10051003', '20301618 ']

29 Nov 2017, Gel status: 1

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for SALL1 were set to Townes-Brocks syndrome, 107480; Townes-Brocks branchiootorenal-like syndrome, 107480; TOWNES-BROCKS SYNDROME (TBS)

29 Nov 2017, Gel status: 1

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for SALL1 were set to Townes-Brocks syndrome, 107480; Townes-Brocks branchiootorenal-like syndrome, 107480; TOWNES-BROCKS SYNDROME (TBS)

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: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

SALL1 was added to Intellectual disabilitypanel. Source: Expert Review Red

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

SALL1 was added to Intellectual disabilitypanel. Sources: Radboud University Medical Center, Nijmegen