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Fetal anomalies

Gene: SMG9

Green List (high evidence)
SMG9 (SMG9, nonsense mediated mRNA decay factor)
EnsemblGeneIds (GRCh38): ENSG00000105771
EnsemblGeneIds (GRCh37): ENSG00000105771
OMIM: 613176, Gene2Phenotype
SMG9 is in 5 panels

4 reviews

Arina Puzriakova (Genomics England Curator)

The rating of this gene has been updated following NHS Genomic Medicine Service approval.
Created: 3 Mar 2022, 11:19 a.m. | Last Modified: 3 Mar 2022, 11:19 a.m.
Panel Version: 1.836
Created: 3 Mar 2022, 11:19 a.m.
Last Modified: 3 Mar 2022, 11:19 a.m.
Panel version: 1.836

Catherine Snow (Genomics England)

Comment on list classification: Change from Green to Amber, as requested by NHSE for signed-off panel.
Created: 19 Aug 2020, 6:23 p.m. | Last Modified: 19 Aug 2020, 6:23 p.m.
Panel Version: 1.87
Created: 19 Aug 2020, 6:23 p.m.
Last Modified: 19 Aug 2020, 6:23 p.m.
Panel version: 1.87

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Three unrelated families, severe multiple congenital malformation syndrome; embryonic lethal in mice.
Created: 27 Feb 2020, 3:27 a.m. | Last Modified: 27 Feb 2020, 3:27 a.m.
Panel Version: 1.3

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Heart and brain malformation syndrome, MIM# 616920

Publications

Created: 27 Feb 2020, 3:27 a.m.
Last Modified: 27 Feb 2020, 3:27 a.m.
Panel version: 1.3

Rebecca Foulger (Genomics England curator)

I don't know

Comment on list classification: Rated probable in Gene2Phenotype for SMG9 Multiple Congenital Anomaly Syndrome based on 2 families in PMID:27018474. Additional family now reported in PMID:31390136. Fetally-relevant phenotype (anomalies detected in-utero) and sufficient cases to support causation. Therefore upgraded from Amber to Green.
Created: 5 May 2020, 3:11 p.m. | Last Modified: 5 May 2020, 3:11 p.m.
Panel Version: 1.42
PMID:31390136. Lecoquierre et al., 2019 performed exome sequencing in a patient with syndromic DD and diverse malformations including cleft lip and palate, facial dysmorphia, brain abnormalities, herat defect, growth retardation and severe infections. She carried a homozygous SMG9 variant, p.(Gln393*). Her unaffected parents were both heterozygous. Phenotypes were first noted in-utero: polyhydamnios, lateral cleft lip and palate, and IUGR noted on ultrasound.
Created: 5 May 2020, 3:10 p.m. | Last Modified: 5 May 2020, 3:10 p.m.
Panel Version: 1.41
PMID:27018474. Shaheen et al, 2016 report 2 consanguineous families with different homozygous LOF variants in SMG9 and and a similar set of congenital anomalies including craniofacial dysmorphism, and major brain and heart malformations.
Created: 5 May 2020, 3:06 p.m. | Last Modified: 5 May 2020, 3:06 p.m.
Panel Version: 1.41
DDG2P rating in original PAGE list: Probable for SMG9 Multiple Congenital Anomaly Syndrome
Created: 11 Dec 2018, 9:05 a.m.
Created: 11 Dec 2018, 9:05 a.m.

Panel version: 1.41

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • PAGE DD-Gene2Phenotype
Phenotypes
  • SMG9 Multiple Congenital Anomaly Syndrome
  • Heart and brain malformation syndrome, 616920
OMIM
613176
Clinvar variants
Variants in SMG9
Penetrance
None
Publications
Panels with this gene

History Filter Activity

3 Mar 2022, Gel status: 3

Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review was removed from gene: SMG9.

3 Mar 2022, Gel status: 3

Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Green was added to SMG9. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

19 Aug 2020, Gel status: 2

Added Tag

Catherine Snow (Genomics England)

Tag for-review tag was added to gene: SMG9.

19 Aug 2020, Gel status: 2

Entity classified by Genomics England curator

Catherine Snow (Genomics England)

Gene: smg9 has been classified as Amber List (Moderate Evidence).

5 May 2020, Gel status: 3

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: SMG9 were set to

5 May 2020, Gel status: 3

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: SMG9 were changed from SMG9 Multiple Congenital Anomaly Syndrome to SMG9 Multiple Congenital Anomaly Syndrome; Heart and brain malformation syndrome, 616920

5 May 2020, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: smg9 has been classified as Green List (High Evidence).

8 Nov 2018, Gel status: 2

Created, Added New Source, Set mode of inheritance, Set Phenotypes

Rebecca Foulger (Genomics England curator)

gene: SMG9 was added gene: SMG9 was added to Fetal anomalies. Sources: PAGE DD-Gene2Phenotype,Expert Review Amber Mode of inheritance for gene: SMG9 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: SMG9 were set to SMG9 Multiple Congenital Anomaly Syndrome