1. Panels
  2. Intellectual disability
  3. SP9
Genes in panel
Prev Next
Regions in panel
Prev Next

Intellectual disability

Gene: SP9

Amber List (moderate evidence)
SP9 (Sp9 transcription factor)
EnsemblGeneIds (GRCh38): ENSG00000217236
EnsemblGeneIds (GRCh37): ENSG00000217236
SP9 is in 3 panels

1 review

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

Comment on list classification: As there is sufficient evidence available (four unrelated cases) for the association of SP9 to developmental delay/ intellectual disability, this gene can be promoted to green rating in the next GMS update.
Created: 30 Jul 2026, 2:32 p.m. | Last Modified: 30 Jul 2026, 2:32 p.m.
Panel Version: 10.85
PMID:38288683 (2024) reported the identification of four different de novo heterozygous variants in SP9 as a cause of a novel form of interneuronopathy in five unrelated cases.

Individual 1 is a male fetus with moderate ventriculomegaly and multiple periventricular and deep gray matter cystic/ischemic lesions (choroid plexus and periventricular cysts, bilateral GE and caudate signal abnormalities with restricted diffusion) identified on late third‑trimester MRI, leading to termination of pregnancy at 35 weeks’ gestation. This individual was identified with c.1133A>C (p.Glu378Ala) variant in SP9 gene.

The age of other four individuals ranged from six months to six years and all had neurodevelopmental disorder of variable severity. A first clinical phenotype consisting of moderate intellectual disability (ID) associated with an ASD with or without epilepsy was present in individuals 2 and 5 who carried frameshift SP9 variants, p.c.1216del (p.His406ThrfsTer2) and c.1192_1207dup (p.Arg403Glnfs∗15), respectively. A second, more severe clinical phenotype consisting of epileptic encephalopathy was present in individuals 3 and 4, who both carried a missense variant c.1133A>G (p.Glu378Gly) involving the same glutamate residue in position 378 as individual 1.

In summary, (global) developmental delay and/or intellectual disability was reported in four patients, while epilepsy was reported in three.

This gene has been associated with relevant phenotype in Gene2Phenotype (with 'moderate' rating on the DD panel), but not yet reported in OMIM (last accessed 30 July 2026).
Sources: Literature
Created: 30 Jul 2026, 2:24 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
neurodevelopmental disorder, MONDO:0700092

Publications

Created: 30 Jul 2026, 2:24 p.m.

Panel version: 10.84

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • neurodevelopmental disorder, MONDO:0700092
Tags
Q3_26_promote_green
Clinvar variants
Variants in SP9
Penetrance
None
Publications
Panels with this gene

History Filter Activity

30 Jul 2026, Gel status: 2

Entity classified by Genomics England curator

Achchuthan Shanmugasundram (Genomics England Curator)

Gene: sp9 has been classified as Amber List (Moderate Evidence).

30 Jul 2026, Gel status: 2

Entity classified by Genomics England curator

Achchuthan Shanmugasundram (Genomics England Curator)

Gene: sp9 has been classified as Amber List (Moderate Evidence).

30 Jul 2026, Gel status: 1

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

Achchuthan Shanmugasundram (Genomics England Curator)

gene: SP9 was added gene: SP9 was added to Intellectual disability. Sources: Literature Q3_26_promote_green tags were added to gene: SP9. Mode of inheritance for gene: SP9 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SP9 were set to 38288683 Phenotypes for gene: SP9 were set to neurodevelopmental disorder, MONDO:0700092 Review for gene: SP9 was set to GREEN