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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q5T280: Variant p.Thr289Met

28S rRNA (uridine-N(3))-methyltransferase
Gene: SPOUT1
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Variant information Variant position: help 289 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help LP/P [Disclaimer] The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance
Residue change: help From Threonine (T) to Methionine (M) at position 289 (T289M, p.Thr289Met). Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.
Physico-chemical properties: help Change from medium size and polar (T) to medium size and hydrophobic (M) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -1 The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:
  • Lowest score: -4 (low probability of substitution).
  • Highest score: 11 (high probability of substitution).
More information can be found on the following page
Variant description: help In NEDGSB; likely pathogenic; partially rescues defects of head development in zebrafish morphants; decreased methyltransferase activity with GAPDH mRNA hairpin as substrate; 2-fold decreased affinity for GAPDH mRNA hairpin. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 289 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 376 The length of the canonical sequence.
Location on the sequence: help CLSAVFAEAPFQDGYDLTIG T SERGSDVASAQLPNFRHALV The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.
Residue conservation: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         CLSAVFAEAPFQDGYDLTIGTSERGSDVASAQLP--NFRHALV

Mouse                         CLSAVFAEAPFQDGYDLTIGTSERGSDVASAQLP--SFRHA

Zebrafish                     CLSAVFSECPYKEGYDLTIGTSEKGQNTDHVTLP--AFRHM

Drosophila                    SMSEIFTKSPYATGYDVTVGTSDRGTNVHEVPNRSYNFNHM
Sequence annotation in neighborhood: help The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:
  • Type: the type of sequence feature.
  • Positions: endpoints of the sequence feature.
  • Description: contains additional information about the feature.
TypePositionsDescription
Chain 1 – 376 28S rRNA (uridine-N(3))-methyltransferase
Binding site 289 – 289
Binding site 292 – 292
Binding site 292 – 292
Beta strand 284 – 295



Literature citations
RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS.
Dharmadhikari A.V.; Abad M.A.; Khan S.; Maroofian R.; Sands T.T.; Ullah F.; Samejima I.; Shen Y.; Wear M.A.; Moore K.E.; Kondakova E.; Mitina N.; Schaub T.; Lee G.K.; Umandap C.H.; Berger S.M.; Iglesias A.D.; Popp B.; Abou Jamra R.; Gabriel H.; Rentas S.; Rippert A.L.; Gray C.; Izumi K.; Conlin L.K.; Koboldt D.C.; Mosher T.M.; Hickey S.E.; Albert D.V.F.; Norwood H.; Lewanda A.F.; Dai H.; Liu P.; Mitani T.; Marafi D.; Eker H.K.; Pehlivan D.; Posey J.E.; Lippa N.C.; Vena N.; Heinzen E.L.; Goldstein D.B.; Mignot C.; de Sainte Agathe J.M.; Al-Sannaa N.A.; Zamani M.; Sadeghian S.; Azizimalamiri R.; Seifia T.; Zaki M.S.; Abdel-Salam G.M.H.; Abdel-Hamid M.S.; Alabdi L.; Alkuraya F.S.; Dawoud H.; Lofty A.; Bauer P.; Zifarelli G.; Afzal E.; Zafar F.; Efthymiou S.; Gossett D.; Towne M.C.; Yeneabat R.; Perez-Duenas B.; Cazurro-Gutierrez A.; Verdura E.; Cantarin-Extremera V.; Marques A.D.V.; Helwak A.; Tollervey D.; Wontakal S.N.; Aggarwal V.S.; Rosenfeld J.A.; Tarabykin V.; Ohta S.; Lupski J.R.; Houlden H.; Earnshaw W.C.; Davis E.E.; Jeyaprakash A.A.; Liao J.;
Nat. Commun. 16:1703-1703(2025)
Cited for: X-RAY CRYSTALLOGRAPHY (2.38 ANGSTROMS) OF 71-376 IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE AND S-ADENOSYL-L-METHIONINE; FUNCTION; SUBUNIT; INVOLVEMENT IN NEDGSB; VARIANTS NEDGSB ASP-86; SER-98; GLN-197; TRP-200; SER-209; SER-244; SER-249 DEL; PRO-256; MET-289; SER-293; PHE-314; 339-TYR--THR-376 DEL; CYS-339; CYS-349; CYS-352; HIS-352 AND MET-353; CHARACTERIZATION OF VARIANTS NEDGSB ASP-86; SER-98; SER-244; MET-289; SER-293 AND MET-353; CHARACTERIZATION OF VARIANT ARG-130; BIOPHYSICOCHEMICAL PROPERTIES; MUTAGENESIS OF ALA-356;
Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.