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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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SP9
Sp9 transcription factor
Chromosome 2 · 2q31.1
NCBI Gene: 100131390Ensembl: ENSG00000217236.2HGNC: HGNC:30690UniProt: P0CG40
7PubMed Papers
20Diseases
0Drugs
5Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
sequence-specific double-stranded DNA bindingDNA-binding transcription factor activity, RNA polymerase II-specificRNA polymerase II cis-regulatory region sequence-specific DNA bindingregulation of transcription by RNA polymerase IIIntellectual disabilityAutistic behaviorEEG abnormalityHypotonia
✦AI Summary

SP9 is a transcription factor of the Krüppel-like factor/specificity protein family that plays a central role in neurodevelopment, particularly in interneuron development and migration 1. SP9 functions as a sequence-specific DNA-binding transcription factor that coordinately regulates gene expression with its homolog Sp8 in the developing nervous system 2. In the postnatal telencephalon, Sp8 and Sp9 coordinately regulate olfactory bulb interneuron development, with double mutants showing reduced interneuron numbers due to defects in neuronal differentiation, tangential and radial migration, and increased cell death, accompanied by failure to express Prokr2 and Tshz1 genes 2. Beyond neural development, SP9 regulates IL-10RB gene expression in the brain, where IL-10RB elevation has been detected in Alzheimer's disease patients and animal models 3. Clinically, de novo heterozygous SP9 variants cause a novel interneuronopathy characterized by intellectual disability, autism spectrum disorder, and epilepsy with variable expressivity 1. Missense variants affecting glutamate 378 produce severe epileptic encephalopathy through hypomorphic and neomorphic DNA-binding effects, whereas loss-of-function variants result in milder phenotypes with epilepsy, developmental delay, and autism spectrum disorder 1.

Sources cited
1
SP9 is a transcription factor belonging to KLF/SP family with central role in interneuron development; de novo variants cause interneuronopathy with intellectual disability, autism, and epilepsy
PMID: 38288683
2
Sp8 and Sp9 coordinately regulate olfactory bulb interneuron development; double mutants show defects in differentiation, migration, cell death, and fail to express Prokr2 and Tshz1
PMID: 28981617
3
Sp8 and Sp9 transcription factors regulate IL-10RB gene expression; IL-10RB is elevated in Alzheimer's disease brain
PMID: 35811529
⚠Limited data available — This gene has 3 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ20
Intellectual disabilityOpen Targets
0.46Moderate
Autistic behaviorOpen Targets
0.42Moderate
EEG abnormalityOpen Targets
0.40Weak
HypotoniaOpen Targets
0.40Weak
hypertensionOpen Targets
0.39Weak
type 2 diabetes mellitusOpen Targets
0.35Weak
Convulsive status epilepticusOpen Targets
0.33Weak
Epileptic spasmOpen Targets
0.33Weak
Epileptic encephalopathyOpen Targets
0.32Weak
essential hypertensionOpen Targets
0.32Weak
neurodegenerative diseaseOpen Targets
0.31Weak
Abnormal caudate nucleus morphologyOpen Targets
0.26Weak
Alzheimer diseaseOpen Targets
0.23Weak
complex neurodevelopmental disorderOpen Targets
0.18Weak
liver diseaseOpen Targets
0.02Suggestive
placental retentionOpen Targets
0.02Suggestive
head and neck squamous cell carcinomaOpen Targets
0.02Suggestive
Miyoshi myopathyOpen Targets
0.01Suggestive
hepatocellular carcinomaOpen Targets
0.01Suggestive
epilepsyOpen Targets
0.01Suggestive
Pathogenic Variants5
NM_001145250.2(SP9):c.245C>A (p.Ser82Ter)Pathogenic
Neurodevelopmental disorder
★☆☆☆2026→ Residue 82
NM_001145250.2(SP9):c.1133A>G (p.Glu378Gly)Pathogenic
Intellectual disability;EEG abnormality;Hypotonia;Epileptic encephalopathy|SP9-associated disorder
★☆☆☆2024→ Residue 378
NM_001145250.2(SP9):c.1133A>C (p.Glu378Ala)Likely pathogenic
Abnormal caudate nucleus morphology;Epileptic encephalopathy;Intellectual disability
☆☆☆☆→ Residue 378
NM_001145250.2(SP9):c.1216del (p.His406fs)Pathogenic
6 conditions
☆☆☆☆→ Residue 406
NM_001145250.2(SP9):c.1192_1207dup (p.Arg403fs)Pathogenic
Autistic behavior;Intellectual disability
☆☆☆☆→ Residue 403
View on ClinVar ↗
Related Genes
ACRV1Protein interaction89%LIPNProtein interaction80%FBXW4Shared pathway25%SP8Co-mentioned in literature20%TBX4Shared pathway17%MBNL1Shared pathway17%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
3%
Heart
0%
Ovary
0%
Liver
0%
Lung
0%
Gene Interaction Network
Click a node to explore
SP9ACRV1LIPNFBXW4SP8TBX4MBNL1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt P0CG40
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.73LoF Tolerant
pLIⓘ
0.58Intermediate
Observed/Expected LoF0.35 [0.18–0.73]
RankingsWhere SP9 stands among ~20K protein-coding genes
  • #17,953of 20,598
    Most Researched7
  • #3,654of 5,498
    Most Pathogenic Variants5
  • #5,694of 17,882
    Most Constrained (LOEUF)0.73
Genes detectedSP9
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
The Effect of Acupuncture and Physiotherapy on Patients with Knee Osteoarthritis: A Randomized Controlled Study.
PMID: 33988943
Pain Physician · 2021
1.00
2
Regulation of the Human IL-10RB Gene Expression by Sp8 and Sp9.
PMID: 35811529
J Alzheimers Dis · 2022
0.90
3
Transcription Factors Sp8 and Sp9 Coordinately Regulate Olfactory Bulb Interneuron Development.
PMID: 28981617
Cereb Cortex · 2018
0.80
4
The
PMID: 38501924
J Virol · 2024
0.70
5
Aborigines and health.
PMID: 4058360
Med J Aust · 1985
0.60