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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9NPE3: Variant p.Thr16Met

H/ACA ribonucleoprotein complex subunit 3
Gene: NOP10
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Variant information Variant position: help 16 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 16 (T16M, p.Thr16Met). 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 CHINE2; likely pathogenic; decreased rRNA pseudouridine synthesis in peripheral blood cells from a homozygous patient; reduced protein abundance in homozygous patient cells; no effect on interaction with DKC1. Any additional useful information about the variant.


Sequence information Variant position: help 16 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 64 The length of the canonical sequence.
Location on the sequence: help MFLQYYLNEQGDRVY T LKKFDPMGQQTCSAHPARFS 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                         MFLQYYLNEQGDRVYTLKKFDPMGQQTCSAHPARFS

Mouse                         MFLQYYLNEQGDRVYTLKKFDPMGQQTCSAHPARFS

Zebrafish                     MFLQFYLNENGERVYTLKKVDPSGQPTSSAHPARFS

Caenorhabditis elegans        MFLRYFLDENQQRVYTLKRTAPSGEQTLTAHPARFS

Drosophila                    MYLMYTINENGDRVYTLKKRTEDGRPTLSAHPARFS

Slime mold                    MHLMYYNDKDGQRVYTLKKESPNHEATYSAHPARFS

Baker's yeast                 MHLMYTLGPDGKRIYTLKKVTESGEITKSAHPARFS

Fission yeast                 MHLMYYLNDEGKRVYTLKKVSPDGRVTKSSHPARFS
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 – 64 H/ACA ribonucleoprotein complex subunit 3
Beta strand 9 – 20



Literature citations
Pseudouridylation defect due to DKC1 and NOP10 mutations causes nephrotic syndrome with cataracts, hearing impairment, and enterocolitis.
Balogh E.; Chandler J.C.; Varga M.; Tahoun M.; Menyhard D.K.; Schay G.; Goncalves T.; Hamar R.; Legradi R.; Szekeres A.; Gribouval O.; Kleta R.; Stanescu H.; Bockenhauer D.; Kerti A.; Williams H.; Kinsler V.; Di W.L.; Curtis D.; Kolatsi-Joannou M.; Hammid H.; Szocs A.; Perczel K.; Maka E.; Toldi G.; Sava F.; Arrondel C.; Kardos M.; Fintha A.; Hossain A.; D'Arco F.; Kaliakatsos M.; Koeglmeier J.; Mifsud W.; Moosajee M.; Faro A.; Javorszky E.; Rudas G.; Saied M.H.; Marzouk S.; Kelen K.; Goetze J.; Reusz G.; Tulassay T.; Dragon F.; Mollet G.; Motameny S.; Thiele H.; Dorval G.; Nuernberg P.; Perczel A.; Szabo A.J.; Long D.A.; Tomita K.; Antignac C.; Waters A.M.; Tory K.;
Proc. Natl. Acad. Sci. U.S.A. 117:15137-15147(2020)
Cited for: VARIANT CHINE2 MET-16; INVOLVEMENT IN CHINE2; CHARACTERIZATION OF VARIANT CHINE2 MET-16; FUNCTION;
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.