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Intellectual disability

Gene: EXT2

Green List (high evidence)

EXT2 (exostosin glycosyltransferase 2)
EnsemblGeneIds (GRCh38): ENSG00000151348
EnsemblGeneIds (GRCh37): ENSG00000151348
OMIM: 608210, Gene2Phenotype
EXT2 is in 15 panels

4 reviews

Rebecca Foulger (Genomics England curator)

Comment on list classification: Updated rating from Amber to Green. Sufficient cases to support causation of MIM:616682, of which ID is a prominent phenotype. Note that I have updated the Mode of Inheritance from AD to AR to match MIM:616682 (and the Genetic epilepsy syndromes panel, #402).
Created: 11 May 2020, 2:30 p.m. | Last Modified: 11 May 2020, 2:30 p.m.
Panel Version: 3.56
PMID:30288735. In 2 siblings with MIM:616682, Gentile et al identified compound het missense variants in EXT2, which segregated with the disorder (D227N and Y608C). The D227N variant contributes to exostosis (inherited from the mother who had a family history of exostosis).
Created: 11 May 2020, 2:21 p.m. | Last Modified: 11 May 2020, 2:27 p.m.
Panel Version: 3.55
PMID:30997052. In a 14 year old girl, Gupta et al. (2019) identified compound het missense variants in the EXT2 gene (V373D and T672M), which segregated with the disorder in the family. The patient also carried a maternal heterozygous variant (R454C) in NDST1. She had developmental delay, autism and epilepsy amongst her phenotypes.
Created: 11 May 2020, 2:21 p.m. | Last Modified: 11 May 2020, 2:21 p.m.
Panel Version: 3.55
PMID:30075207. In 2 brothers, born of consanguineous Syrian parents, with MIM:616682 El-Bazzal et al. (2019) identified a homozygous missense mutation in the EXT2 gene (p.Ser4Leu). Psychomotor delay was noted for both at the age of 3 months.
Created: 11 May 2020, 2:21 p.m. | Last Modified: 11 May 2020, 2:21 p.m.
Panel Version: 3.55
PMID:26246518: In 4 siblings, born of consanguineous parents in the Old Order Mennonite community, with seizures, scoliosis, and macrocephaly/microcephaly syndrome (MIM:616682), Farhan et al. (2015) identified homozygosity for 2 missense mutations in EXT2 (M87R and R95C). All siblings had moderate ID and a seizure disorder.
Created: 11 May 2020, 2:20 p.m. | Last Modified: 11 May 2020, 2:20 p.m.
Panel Version: 3.55
Comment on mode of inheritance: Updated MOI from MONOALLELIC to BIALLELIC. EXT2 is associated with 2 different disorders: Seizures, scoliosis, and macrocephaly syndrome, 616682 (AR) and Exostoses, multiple, type 2, 133701 (AD). MIM:616682 is relevant to this panel.
Created: 11 May 2020, 2:08 p.m. | Last Modified: 11 May 2020, 2:08 p.m.
Panel Version: 3.54

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Bi-alllelic missense variants cause a syndromic ID condition. Note heterozygous variants (mostly causing premature termination) cause multiple exostoses.
Created: 2 Feb 2020, 5:03 a.m. | Last Modified: 2 Feb 2020, 5:03 a.m.
Panel Version: 3.0

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Seizures, scoliosis, and macrocephaly syndrome, MIM#616682

Mode of pathogenicity
Other

Variants in this GENE are reported as part of current diagnostic practice

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 . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 5:41 p.m.

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

Publications

Louise Daugherty (Genomics England Curator)

Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to access inclusion and pertinence to this panel.
Created: 28 Jul 2017, 11:15 a.m.

History Filter Activity

11 May 2020, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: ext2 has been classified as Green List (High Evidence).

11 May 2020, Gel status: 2

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: EXT2 were changed from Seizures, scoliosis, and macrocephaly syndrome, 616682 to Seizures, scoliosis, and macrocephaly syndrome, 616682; autosomal recessive EXT2-related syndrome

11 May 2020, Gel status: 2

Set mode of inheritance

Rebecca Foulger (Genomics England curator)

Mode of inheritance for gene: EXT2 was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal

11 May 2020, Gel status: 2

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: EXT2 were set to 25529582; 26246518; 30997052; 30288735

11 May 2020, Gel status: 2

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: EXT2 were changed from Exostoses, multiple, type 2, 133701 to Seizures, scoliosis, and macrocephaly syndrome, 616682

11 May 2020, Gel status: 2

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: EXT2 were set to 25529582

11 May 2020, Gel status: 2

Set mode of inheritance

Rebecca Foulger (Genomics England curator)

Mode of inheritance for gene: EXT2 was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal

11 May 2020, Gel status: 2

Set mode of inheritance

Rebecca Foulger (Genomics England curator)

Mode of inheritance for gene: EXT2 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BIALLELIC, autosomal or pseudoautosomal

11 May 2020, Gel status: 2

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: EXT2 were set to

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.

28 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).

27 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

EXT2 was created by BRIDGE

27 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

EXT2 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene