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  3. SCUBE3
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Fetal anomalies

Gene: SCUBE3

Green List (high evidence)
SCUBE3 (signal peptide, CUB domain and EGF like domain containing 3)
EnsemblGeneIds (GRCh38): ENSG00000146197
EnsemblGeneIds (GRCh37): ENSG00000146197
OMIM: 614708, Gene2Phenotype
SCUBE3 is in 5 panels

5 reviews

Stephanie Allen (Birmingham Women's NHS Foundation Trust)

This gene and phenotype were reviewed during a meeting on 2nd March 2023 between representatives of the North Thames and Central & South R21 testing GLHs. Clinical review and curation was performed by Lyn Chitty, (North Thames GLH), and Stephanie Allen, Denise Williams, Anna de Burca and Megan Horton-Bell (Central & South GLH). Outcome of review: Confirmed that the phenotype is fetally relevant, support adding to the Fetal anomalies panel as a Green gene.
Created: 5 May 2023, 3 p.m. | Last Modified: 5 May 2023, 3 p.m.
Panel Version: 3.8
Created: 5 May 2023, 3 p.m.
Last Modified: 5 May 2023, 3 p.m.
Panel version: 3.8

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to Green and the mode of inheritance set to BIALLELIC, autosomal or pseudoautosomal following NHS Genomic Medicine Service approval.
Created: 10 Oct 2023, 3:39 p.m. | Last Modified: 10 Oct 2023, 3:39 p.m.
Panel Version: 3.111
Associated with relevant phenotype in OMIM and as probable Gen2Phen gene. PMID 33308444 reports eight SCUBE variants in nine unrelated families, including eighteen affected members. In vtro studies demonstrated a variable impact of disease-causing variants on transcript processing, protein secretion and function, resulting in dysregulation on bone morphogenetic protein (BMP) signaling and a Scube3−/− mouse showed shared phenotypic features with OMIM:619184. Prenatal growth retardation was evident in 8/11 relevant cases.
Created: 1 Apr 2021, 10:58 a.m. | Last Modified: 14 Oct 2021, 10:21 a.m.
Panel Version: 1.727
Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
Created: 1 Apr 2021, 10:55 a.m. | Last Modified: 1 Apr 2021, 10:55 a.m.
Panel Version: 2.85

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Created: 1 Apr 2021, 10:55 a.m.
Last Modified: 14 Oct 2021, 10:21 a.m.
Copied from panel: Skeletal dysplasia v2.136

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Eighteen affected individuals from nine unrelated families reported with a consistent phenotype characterised by reduced growth, skeletal features, distinctive craniofacial appearance, and dental anomalies. Mouse model recapitulated phenotype.
Created: 7 Jan 2021, 9:56 a.m. | Last Modified: 7 Jan 2021, 9:56 a.m.
Panel Version: 2.42

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Short stature; skeletal abnormalities; craniofacial abnormalities; dental anomalies

Publications

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

Created: 7 Jan 2021, 9:56 a.m.
Last Modified: 7 Jan 2021, 9:56 a.m.
Copied from panel: Skeletal dysplasia v2.136

Arina Puzriakova (Genomics England Curator)

Comment on list classification: Confirmed with Stephanie Allen that the GMS Fetal expert group determined there is sufficient evidence to classify this gene as Green (9th May 2023).
Created: 10 May 2023, 10:44 a.m. | Last Modified: 10 May 2023, 10:44 a.m.
Panel Version: 3.80
The to_be_confirmed_NHSE tag has been added, as further NHSE review is required before promoting this gene to green.
Created: 30 Jan 2023, 4:26 p.m. | Last Modified: 30 Jan 2023, 4:26 p.m.
Panel Version: 2.10
Comment on list classification: Rating Red as currently only one case reported with a potentially pathogenic variant associated with skeletal dysplasia. Additional cases required to corroborate causality.
Created: 6 Nov 2020, 5:39 p.m. | Last Modified: 6 Nov 2020, 5:39 p.m.
Panel Version: 2.30
Created: 6 Nov 2020, 5:39 p.m.
Last Modified: 6 Nov 2020, 5:39 p.m.
Copied from panel: Skeletal dysplasia v2.136

Eleanor Williams (Genomics England Curator)

Updating tags to be Q3_22_expert_review and Q3_22_rating so that gene is included in the next GMS report (Oct 2022)
Created: 5 Oct 2022, 4:59 p.m. | Last Modified: 5 Oct 2022, 4:59 p.m.
Panel Version: 1.974
A variant in this gene has been found in a 100K proband as potentially being the cause of a skeletal dysplasia.
Created: 14 Jan 2020, 3:47 p.m. | Last Modified: 14 Jan 2020, 3:48 p.m.
Panel Version: 2.0
Created: 14 Jan 2020, 3:47 p.m.
Last Modified: 14 Jan 2020, 3:48 p.m.
Copied from panel: Skeletal dysplasia v2.136

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • Expert Review Green
  • Other
Phenotypes
  • Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies OMIM:619184
  • short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2 MONDO:0030953
OMIM
614708
Clinvar variants
Variants in SCUBE3
Penetrance
unknown
Publications
Panels with this gene

History Filter Activity

10 Oct 2023, Gel status: 3

Removed Tag, Removed Tag

Sarah Leigh (Genomics England Curator)

Tag Q2_23_promote_green was removed from gene: SCUBE3. Tag Q2_23_NHS_review was removed from gene: SCUBE3.

10 Oct 2023, Gel status: 3

Added New Source, Added New Source, Status Update

Sarah Leigh (Genomics England Curator)

Source Expert Review Green was added to SCUBE3. Source NHS GMS was added to SCUBE3. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

10 May 2023, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: scube3 has been classified as Amber List (Moderate Evidence).

10 May 2023, Gel status: 2

Removed Tag, Removed Tag, Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag to_be_confirmed_NHSE was removed from gene: SCUBE3. Tag Q3_22_rating was removed from gene: SCUBE3. Tag Q3_22_expert_review was removed from gene: SCUBE3.

5 May 2023, Gel status: 2

Added Tag, Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q2_23_promote_green tag was added to gene: SCUBE3. Tag Q2_23_NHS_review tag was added to gene: SCUBE3.

30 Jan 2023, Gel status: 2

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag to_be_confirmed_NHSE tag was added to gene: SCUBE3.

5 Oct 2022, Gel status: 2

Removed Tag, Added Tag, Added Tag

Eleanor Williams (Genomics England Curator)

Tag Q4_21_expert_review was removed from gene: SCUBE3. Tag Q3_22_rating tag was added to gene: SCUBE3. Tag Q3_22_expert_review tag was added to gene: SCUBE3.

14 Oct 2021, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: SCUBE3 were changed from Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies OMIM:619184 to Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies OMIM:619184; short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2 MONDO:0030953

14 Oct 2021, Gel status: 2

Added Tag

Sarah Leigh (Genomics England Curator)

Tag Q4_21_expert_review tag was added to gene: SCUBE3.

14 Oct 2021, Gel status: 2

Removed Tag

Sarah Leigh (Genomics England Curator)

Tag Q2_21_rating was removed from gene: SCUBE3.

14 Oct 2021, Gel status: 2

Created, Added New Source, Added Tag, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Sarah Leigh (Genomics England Curator)

gene: SCUBE3 was added gene: SCUBE3 was added to Fetal anomalies. Sources: Expert Review Amber,Other Q2_21_rating tags were added to gene: SCUBE3. Mode of inheritance for gene: SCUBE3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SCUBE3 were set to 33308444 Phenotypes for gene: SCUBE3 were set to Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies OMIM:619184 Penetrance for gene: SCUBE3 were set to unknown