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Intellectual disability

Gene: SOX9

Amber List (moderate evidence)
SOX9 (SRY-box 9)
EnsemblGeneIds (GRCh38): ENSG00000125398
EnsemblGeneIds (GRCh37): ENSG00000125398
OMIM: 608160, Gene2Phenotype
SOX9 is in 10 panels

6 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

I don't know

The rating of this gene has been updated to amber following NHS Genomic Medicine Service approval.
Created: 26 Sep 2024, 2:57 p.m. | Last Modified: 26 Sep 2024, 2:57 p.m.
Panel Version: 7.41
Created: 26 Sep 2024, 2:57 p.m.
Last Modified: 26 Sep 2024, 2:57 p.m.
Panel version: 7.41

Sarah Leigh (Genomics England Curator)

I don't know

Based on review by Tracy Lester (Genetics laboratory, Oxford UK) and a literature review, there is insufficient evidence for an association between SOX9 variants and intellectual disability.
Created: 25 Jun 2024, 10:54 a.m. | Last Modified: 25 Jun 2024, 10:54 a.m.
Panel Version: 6.40
Created: 25 Jun 2024, 10:54 a.m.
Last Modified: 25 Jun 2024, 10:54 a.m.
Panel version: 6.40

Tracy Lester (Genetics laboratory, Oxford UK)

I don't know

I don't think there is sufficient evidence for this gene to be included on the R29 panel as a green gene. Just 2 cases referenced - the first is said to have mild ID and the second has speech delay but is also severely deaf, There is developmental delay in motor skills in both but it is unclear if this is related to the skeletal problems (which are their primary feature). The link between this gene and intellectual disability is not currently proven and this gene should be amber for R29. The gene should remain green for R104 and other panels.
Created: 14 Mar 2024, 5:20 p.m. | Last Modified: 14 Mar 2024, 5:20 p.m.
Panel Version: 5.497

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Skeletal dysplasia

Created: 14 Mar 2024, 5:20 p.m.
Last Modified: 14 Mar 2024, 5:20 p.m.
Panel version: 5.497

Rachel Jones (GSTT)

Green List (high evidence)

SOX9 mutations usually cause campomelic dysplasia, or acampomelic dysplasia, with short ribs and bowed long bones. SOX 9 is already on skeletal dysplasia and clefting panels in green.

However there are some papers that have identified patients with milder phenotypes

PMID: 24704791 - patient with Pierre-Robin and talipes, some facial dysmorphic features, severe deafness, compatible with a Collagen disorder plus severe intellectual disability

PMID: 21373255 - patient with features of a skeletal dysplasia (including short stature), intellectual disability, mild hearing loss, micrognathia and a high palate. Same paper gives clinical summary of other surviving patients with mild campomelic dysplasia/SOX9 mutations. 90% have a skeletal dysplasia (short stature/short limbs, 50% with bowing of the long bones) and 84% intellectual disability, 50% with hearing impairment.

Some of these patients may present as syndromic ID with short limbs therefore I feel it is appropriate to promote to green on ID panel.
Created: 24 Apr 2018, 3:03 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Publications

Created: 24 Apr 2018, 3:03 p.m.

Panel version: 2.46

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 : Cis-regulatory or promotor mutation; Loss of function
Created: 27 Jul 2017, 8:32 p.m.

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

Publications

Created: 2 Aug 2017, 10:52 p.m.

Panel version: 1.354

Louise Daugherty (Genomics England Curator)

Comment on publications: added new publications to support ID phenotype from internal clinical review
Created: 25 Apr 2018, 12:13 p.m.
Comment on list classification: Promoted from Amber to Green as a result of internal clinical review
Created: 25 Apr 2018, 12:11 p.m.
Comment on list classification: Promoted from Amber to Green as a result of internal clinical review
Created: 25 Apr 2018, 12:11 p.m.
Comment on mode of inheritance: changed MOI in view of internal clinical review
Created: 25 Apr 2018, 12:11 p.m.
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, 4:09 p.m.
Created: 28 Jul 2017, 4:09 p.m.

Panel version: 1.326

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • NHS GMS
  • Expert Review Amber
Phenotypes
  • Campomelic dysplasia with autosomal sex reversal, OMIM:114290
  • Acampomelic campomelic dysplasia, OMIM:114290
  • Campomelic dysplasia, OMIM:114290
  • campomelic dysplasia, MONDO:0007251
OMIM
608160
Clinvar variants
Variants in SOX9
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

26 Sep 2024, Gel status: 2

Removed Tag, Removed Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q2_24_demote_amber was removed from gene: SOX9. Tag Q2_24_NHS_review was removed from gene: SOX9.

26 Sep 2024, Gel status: 2

Added New Source, Added New Source, Status Update

Achchuthan Shanmugasundram (Genomics England Curator)

Source Expert Review Amber was added to SOX9. Source NHS GMS was added to SOX9. Rating Changed from Green List (high evidence) to Amber List (moderate evidence)

25 Jun 2024, Gel status: 3

Added Tag, Added Tag

Sarah Leigh (Genomics England Curator)

Tag Q2_24_demote_amber tag was added to gene: SOX9. Tag Q2_24_NHS_review tag was added to gene: SOX9.

25 Jun 2024, Gel status: 3

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: SOX9 were changed from Campomelic dysplasia with autosomal sex reversal, 114290; Acampomelic campomelic dysplasia, 114290; Campomelic dysplasia, 114290; intellectual disability to Campomelic dysplasia with autosomal sex reversal, OMIM:114290; Acampomelic campomelic dysplasia, OMIM:114290; Campomelic dysplasia, OMIM:114290; campomelic dysplasia, MONDO:0007251

25 Apr 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for SOX9 were set to Campomelic dysplasia with autosomal sex reversal, 114290; Acampomelic campomelic dysplasia, 114290; Campomelic dysplasia, 114290; intellectual disability

25 Apr 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for SOX9 were set to 25529582; 21373255; 24704791

25 Apr 2018, Gel status: 3

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

25 Apr 2018, Gel status: 3

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

25 Apr 2018, Gel status: 2

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for SOX9 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

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

Added New Source

BRIDGE consortium (NIHRBR-RD)

SOX9 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

27 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

SOX9 was created by BRIDGE