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Intellectual disability

Gene: SPART

Green List (high evidence)

SPART (spartin)
EnsemblGeneIds (GRCh38): ENSG00000133104
EnsemblGeneIds (GRCh37): ENSG00000133104
OMIM: 607111, Gene2Phenotype
SPART is in 10 panels

4 reviews

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Although primarily a HSP presentation, Table 1 in PMID 20437587 summarises the clinical features in cases to date. There is delayed language acquisition and motor skills, almost universally, alongside poor school performance and therefore on balance, it should be included. However, I accept that the diagnostic confidence in the absence of spasticity will be limited.
Created: 14 Nov 2017, 9:42 a.m.

Rebecca Foulger (Genomics England curator)

Green List (high evidence)

Rated Green based on >3 unrelated cases of SPG20 homozygous variants causing Troyer syndrome (MIM:275900), which includes developmental delay. PMID:28679690 presents a recent (2017) case and summary. Biallelic MOI supported by OMIM.
Created: 29 Nov 2017, 11:19 a.m.
Dardour et al. (2017, PMID:28679690) report 3 brothers of a conanguineous Moroccan family with severe ID and a homozygous c.1369C>T (p.Arg457*) variant in SPG20.
Created: 19 Sep 2017, 2:30 p.m.
Tawamie et al. (2015, PMID:26003402) reported 2 sibs, born of consanguineous Turkish parents, with complicated spastic paraplegia. The patients were 26 and 17 years of age at the time of the report. The older sister had delayed psychomotor development in infancy. Her IQ was 46. Her brother had developmental delay. They identified the c.364delAT in exon 2 of SPG20, and haplotype analysis confirmed that the variant occurred independently of the same variation reported by Manzini.
Created: 19 Sep 2017, 2:30 p.m.
Manzini et al. (2010, PMID:20437587) reported a large Omani kindred with SPG20. All affected individuals presented with short stature and dysarthria, and showed delayed motor and cognitive development. A 2bp deletion (c.364_365delAT) was identified in the first coding exon of SPG20, resulting in a frameshift and premature termination. Unaffected indivs were heterozygous.
Created: 19 Sep 2017, 2:29 p.m.
Bakowska et al. (2008, PMID:18413476) reported an Amish brother and sister from Ohio with Troyer syndrome (MIM:275900). Both showed delayed motor and cognitive development and developed a progressive deterioration in gait and speech during childhood. The SPG20 1110delA mutation was present in both siblings.
Created: 19 Sep 2017, 2:28 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Troyer syndrome (MIM:275900); developmental delay

Publications

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_movement_disorder_list . Main mutation mechanism : NA
Created: 27 Jul 2017, 8:33 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : 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, 1:26 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

  • Personal communication with NIHRBRRD BRIDGE SPEED

Louise Daugherty (Genomics England Curator)

Comment on phenotypes: fixed format
Created: 19 Dec 2017, 5:01 p.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, 2:05 p.m.
added new-gene-name tag, new approved HGNC gene symbol is SPART
Created: 19 Jul 2017, 4:29 p.m.

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.

19 Dec 2017, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for SPART were set to Troyer syndrome; MIM:275900; developmental delay

29 Nov 2017, Gel status: 4

Added New Source, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Green was added to SPART. Panel: Intellectual disability Publications for gene SPART was set to ['18413476', ' 20437587', ' 26003402', ' 28679690']

5 Nov 2017, Gel status: 2

Changed Gene Name

GEL ()

SPG20 was changed to SPART

5 Nov 2017, Gel status: 2

Removed Tag

GEL ()

new-gene-name was removed from SPG20. Panel: Intellectual disability

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)

SPG20 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

SPG20 was created by BRIDGE