HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
5 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SPOUT1
SPOUT domain containing methyltransferase 1
Chromosome 9 · 9q34.11
NCBI Gene: 51490Ensembl: ENSG00000198917.14HGNC: HGNC:26933UniProt: Q5T280
64PubMed Papers
21Diseases
0Drugs
6Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
spindle pole centrosomemitotic spindleprotein bindingmethyltransferase activityneurodevelopmental disorder with poor growth, seizures, and brain abnormalitiesNeurodevelopmental disorderundetermined early-onset epileptic encephalopathyChronic Obstructive Asthma
✦AI Summary

SPOUT1 is an S-adenosyl-L-methionine-dependent RNA methyltransferase that catalyzes N3 methylation of uridine in 28S rRNA 1. Beyond its catalytic function, SPOUT1 serves a critical structural role in mitosis by maintaining centrosome attachment to spindle poles during metaphase and promoting chromosome 9 23. The protein likely facilitates centrosome maturation by recruiting AKAP9 to centrosomes in early mitosis 3. Additionally, SPOUT1 regulates miRNA-145 expression through direct hairpin binding and post-transcriptional mechanisms 4. Bi-allelic SPOUT1 variants cause SpADMiSS (SPOUT1 Associated Development delay Microcephaly Seizures Short stature), an autosomal recessive neurodevelopmental disorder 56. Disease-associated missense variants cluster in the catalytic domain, exhibiting reduced methyltransferase activity and compromised centrosome tethering 5. In zebrafish models, spout1 mutations produce microcephaly with increased apoptosis, likely reflecting defective cell cycle progression 5. The dual functionality of SPOUT1—combining RNA modification with mitotic spindle organization—explains how catalytic mutations cause both molecular and cellular phenotypes underlying neurodevelopmental disease.

Sources cited
1
SPOUT1 is an S-adenosyl-L-methionine-dependent RNA methyltransferase that catalyzes m3U modification at the N3 position of uridine in 28S rRNA
PMID: 39671501
2
SPOUT1 (CENP-32) is required for centrosome association with spindle poles and chromosome alignment during metaphase
PMID: 20813266
3
CENP-32/SPOUT1 is required for centrosomes to maintain centrosomal dominance and integrate into functional spindles; may promote centrosome maturation by recruiting AKAP9
PMID: 25657325
4
SPOUT1 binds specifically to miRNA MIR145 hairpin and regulates MIR145 expression at post-transcriptional level
PMID: 28431233
5
Bi-allelic SPOUT1 variants cause SpADMiSS neurodevelopmental disorder characterized by developmental delay, microcephaly, seizures, and short stature; disease variants have reduced methyltransferase activity and compromised centrosome tethering
PMID: 39962046
6
SPOUT1 pathogenic variants are associated with neurodevelopmental disorder underpinned by mitotic spindle organization defects and chromosome segregation errors; zebrafish models show microcephaly and apoptosis
PMID: 38260255
Disease Associationsⓘ21
neurodevelopmental disorder with poor growth, seizures, and brain abnormalitiesOpen Targets
0.47Moderate
Neurodevelopmental disorderOpen Targets
0.41Moderate
undetermined early-onset epileptic encephalopathyOpen Targets
0.27Weak
Chronic Obstructive AsthmaOpen Targets
0.12Weak
hypothyroidismOpen Targets
0.11Weak
response to statinOpen Targets
0.09Suggestive
allergic diseaseOpen Targets
0.02Suggestive
microcephalyOpen Targets
0.01Suggestive
ulcerative colitisOpen Targets
0.01Suggestive
epilepsyOpen Targets
0.01Suggestive
Neurodevelopmental delayOpen Targets
0.01Suggestive
Epileptic encephalopathyOpen Targets
0.01Suggestive
dentin dysplasiaOpen Targets
0.01Suggestive
Global developmental delayOpen Targets
0.01Suggestive
Intellectual disabilityOpen Targets
0.01Suggestive
cancerOpen Targets
0.01Suggestive
neoplasmOpen Targets
0.01Suggestive
cervical squamous intraepithelial neoplasiaOpen Targets
0.00Suggestive
developmental and epileptic encephalopathyOpen Targets
0.00Suggestive
Fanconi anemiaOpen Targets
0.00Suggestive
Neurodevelopmental disorder with poor growth, seizures, and brain abnormalitiesUniProt
Pathogenic Variants6
NM_016390.4(SPOUT1):c.292G>A (p.Gly98Ser)Likely pathogenic
Neurodevelopmental disorder|Undetermined early-onset epileptic encephalopathy|Neurodevelopmental disorder with poor growth, seizures, and brain abnormalities
★★☆☆2025→ Residue 98
NM_016390.4(SPOUT1):c.940C>T (p.Leu314Phe)Likely pathogenic
Neurodevelopmental disorder
★☆☆☆2024→ Residue 314
NM_016390.4(SPOUT1):c.730G>A (p.Gly244Ser)Likely pathogenic
Neurodevelopmental disorder|Neurodevelopmental disorder with poor growth, seizures, and brain abnormalities
★☆☆☆2024→ Residue 244
NM_016390.4(SPOUT1):c.877G>A (p.Gly293Ser)Likely pathogenic
Neurodevelopmental disorder
★☆☆☆2024→ Residue 293
NM_016390.4(SPOUT1):c.1016A>G (p.Tyr339Cys)Likely pathogenic
Neurodevelopmental disorder
★☆☆☆2024→ Residue 339
NM_016390.4(SPOUT1):c.1054C>T (p.Arg352Cys)Likely pathogenic
Neurodevelopmental disorder
★☆☆☆2024→ Residue 352
View on ClinVar ↗
Related Genes
UTP11Protein interaction100%WDR46Protein interaction100%TBC1D13Protein interaction94%KYAT1Protein interaction93%ENDOGProtein interaction89%PISDProtein interaction72%
Tissue Expression6 tissues
Liver
100%
Ovary
75%
Bone Marrow
66%
Lung
54%
Heart
47%
Brain
37%
Gene Interaction Network
Click a node to explore
SPOUT1UTP11WDR46TBC1D13KYAT1ENDOGPISD
PROTEIN STRUCTURE
Preparing viewer…
PDB4RG1 · 1.86 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.98LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.76 [0.59–0.98]
RankingsWhere SPOUT1 stands among ~20K protein-coding genes
  • #7,318of 20,598
    Most Researched64
  • #3,373of 5,498
    Most Pathogenic Variants6
  • #9,304of 17,882
    Most Constrained (LOEUF)0.98
Genes detectedSPOUT1
Sources retrieved5 papers
Response time—
📄 Sources
5
1
RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS.
PMID: 39962046
Nat Commun · 2025
1.00
2
The Ptch/SPOUT1 methyltransferase deposits an m
PMID: 39671501
Sci Adv · 2024
0.80
3
Malakoplakia with aberrant ALK expression by immunohistochemistry: a case report.
PMID: 37644531
Diagn Pathol · 2023
0.60
4
CENP-32 is required to maintain centrosomal dominance in bipolar spindle assembly.
PMID: 25657325
Mol Biol Cell · 2015
0.40
5
RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS.
PMID: 38260255
medRxiv · 2024
0.20