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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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SPEN
spen family transcriptional repressor
Chromosome 1 Β· 1p36.21-p36.13
NCBI Gene: 23013Ensembl: ENSG00000065526.13HGNC: HGNC:17575UniProt: Q96T58
128PubMed Papers
21Diseases
0Drugs
101Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
transcription repressor complextranscription corepressor activityRNA bindingrandom inactivation of X chromosomeRadio-Tartaglia syndromeneurodegenerative diseasegenetic disorderchronic lymphocytic leukemia
✦AI Summary

SPEN (spen family transcriptional repressor) is a nuclear transcriptional regulatory protein that functions as both a corepressor and transcriptional platform. SPEN acts as a negative regulator of the Notch signaling pathway by interacting with RBPSUH to prevent NOTCH1-mediated transactivation 1. The protein recruits histone deacetylase-containing complexes to mediate transcriptional repression and plays a critical role in X chromosome 1, where it nucleates supramolecular complexes (SMACs) containing multiple SPEN molecules that generate local protein gradients to propagate silencing across X-linked genes 2. SPEN interacts with the Xist lncRNA through its A-repeat domain and is essential for Xist-mediated gene silencing and chr1 modifications 3. SPEN haploinsufficiency causes a neurodevelopmental disorder with significant clinical overlap to proximal 1p36 deletion syndrome, presenting with developmental delay, intellectual disability, autism spectrum disorder, brain anomalies, congenital heart defects, and distinctive X chromosome 1 methylation episignatures in females 1. The gene's involvement in neurodevelopmental disorders is supported by large-scale sequencing studies identifying SPEN among genes enriched for de novo mutations in autism and other neurodevelopmental conditions 4. Additionally, SPEN mutations have been identified in prostate cancer genomics 5, suggesting broader roles in oncogenic pathways.

Sources cited
1
SPEN haploinsufficiency causes neurodevelopmental disorder overlapping proximal del1p36 syndrome with features including developmental delay, autism, heart defects, and distinctive X chromosome episignatures
PMID: 33596411
2
SPEN nucleates supramolecular complexes containing multiple SPEN molecules that generate protein gradients to propagate X chromosome silencing
PMID: 34813726
3
SPEN (Drosophila Split ends homolog) interacts with Xist lncRNA via A-repeat domain and is required for Xist-mediated gene silencing
PMID: 25843628
4
SPEN identified among genes enriched for de novo mutations in neurodevelopmental disorders including autism
PMID: 33004838
5
SPEN identified as significantly mutated gene in prostate cancer genomic analysis
PMID: 29610475
Disease Associationsβ“˜21
Radio-Tartaglia syndromeOpen Targets
0.75Strong
neurodegenerative diseaseOpen Targets
0.55Moderate
genetic disorderOpen Targets
0.54Moderate
chronic lymphocytic leukemiaOpen Targets
0.47Moderate
diffuse large B-cell lymphomaOpen Targets
0.47Moderate
developmental disorder of mental healthOpen Targets
0.46Moderate
Neurodevelopmental delayOpen Targets
0.41Moderate
melanomaOpen Targets
0.38Weak
colorectal adenocarcinomaOpen Targets
0.37Weak
urinary bladder carcinomaOpen Targets
0.37Weak
bile duct carcinomaOpen Targets
0.37Weak
carcinoma of liver and intrahepatic biliary tractOpen Targets
0.37Weak
cutaneous melanomaOpen Targets
0.37Weak
Endometrial Endometrioid AdenocarcinomaOpen Targets
0.37Weak
lung carcinomaOpen Targets
0.37Weak
nodular melanomaOpen Targets
0.37Weak
Ovarian Endometrioid Adenocarcinoma with Squamous DifferentiationOpen Targets
0.37Weak
skin basal cell carcinomaOpen Targets
0.37Weak
skin squamous cell carcinomaOpen Targets
0.37Weak
superficial spreading melanomaOpen Targets
0.37Weak
Radio-Tartaglia syndromeUniProt
Pathogenic Variants101
NM_015001.3(SPEN):c.1603C>T (p.Arg535Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 535
NM_015001.3(SPEN):c.3508C>T (p.Arg1170Ter)Pathogenic
not provided|Radio-Tartaglia syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 1170
NM_015001.3(SPEN):c.9502C>T (p.Arg3168Ter)Likely pathogenic
Radio-Tartaglia syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 3168
NM_015001.3(SPEN):c.6641del (p.Glu2214fs)Pathogenic
Inborn genetic diseases|Radio-Tartaglia syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 2214
NM_015001.3(SPEN):c.2417_2418dup (p.Arg807fs)Pathogenic
Neurodevelopmental abnormality|not provided|Radio-Tartaglia syndrome|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 807
NM_015001.3(SPEN):c.922C>T (p.Arg308Ter)Pathogenic
Radio-Tartaglia syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 308
NM_015001.3(SPEN):c.7232C>A (p.Ser2411Ter)Pathogenic
Autism spectrum disorder|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 2411
NM_015001.3(SPEN):c.7024C>T (p.Arg2342Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 2342
NM_015001.3(SPEN):c.6223_6227del (p.Ser2075fs)Pathogenic
not provided|Radio-Tartaglia syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 2075
NM_015001.3(SPEN):c.3721C>T (p.Arg1241Ter)Pathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 1241
NM_015001.3(SPEN):c.3793C>T (p.Arg1265Ter)Pathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 1265
NM_015001.3(SPEN):c.6641_6642del (p.Glu2214fs)Pathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2021β†’ Residue 2214
NM_015001.3(SPEN):c.6974_6975del (p.Leu2325fs)Pathogenic
Inborn genetic diseases|Radio-Tartaglia syndrome|not provided
β˜…β˜…β˜†β˜†2021β†’ Residue 2325
NM_015001.3(SPEN):c.6087_6088del (p.Glu2029fs)Pathogenic
Radio-Tartaglia syndrome|not provided|Encephalopathy
β˜…β˜…β˜†β˜†2020β†’ Residue 2029
NM_015001.3(SPEN):c.7009C>T (p.Arg2337Ter)Likely pathogenic
Radio-Tartaglia syndrome
β˜…β˜†β˜†β˜†2026β†’ Residue 2337
NM_015001.3(SPEN):c.6973_6974del (p.Leu2325fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 2325
NM_015001.3(SPEN):c.8819_8820del (p.Pro2940fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 2940
NM_015001.3(SPEN):c.70G>T (p.Glu24Ter)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 24
NM_015001.3(SPEN):c.8545C>T (p.Gln2849Ter)Likely pathogenic
Radio-Tartaglia syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 2849
NM_015001.3(SPEN):c.5130_5133del (p.Glu1711fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 1711
View on ClinVar β†—
Related Genes
HDAC1Protein interaction100%NOTCH1Protein interaction100%RBPJProtein interaction90%NCOR2Protein interaction90%MSX2Protein interaction89%CTBP1Protein interaction82%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
77%
Lung
62%
Brain
47%
Liver
43%
Heart
36%
Gene Interaction Network
Click a node to explore
SPENHDAC1NOTCH1RBPJNCOR2MSX2CTBP1
PROTEIN STRUCTURE
Preparing viewer…
PDB7Z1K Β· 1.55 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.09Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.06 [0.04–0.09]
RankingsWhere SPEN stands among ~20K protein-coding genes
  • #3,666of 20,598
    Most Researched128 Β· top quartile
  • #766of 5,498
    Most Pathogenic Variants101 Β· top quartile
  • #44of 17,882
    Most Constrained (LOEUF)0.09 Β· top 1%
Genes detectedSPEN
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders.
PMID: 33004838
Nat Commun Β· 2020
1.00
2
Consensus statement: Academy of Nutrition and Dietetics and American Society for Parenteral and Enteral Nutrition: characteristics recommended for the identification and documentation of adult malnutrition (undernutrition).
PMID: 22535923
JPEN J Parenter Enteral Nutr Β· 2012
0.90
3
Systematic discovery of Xist RNA binding proteins.
PMID: 25843628
Cell Β· 2015
0.80
4
1p36 deletion syndrome: an update.
PMID: 26345236
Appl Clin Genet Β· 2015
0.70
5
RNA promotes the formation of spatial compartments in the nucleus.
PMID: 34739832
Cell Β· 2021
0.60