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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q96Q11: Variant p.Ile223Thr

CCA tRNA nucleotidyltransferase 1, mitochondrial
Gene: TRNT1
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Variant information Variant position: help 223 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 Isoleucine (I) to Threonine (T) at position 223 (I223T, p.Ile223Thr). 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 hydrophobic (I) to medium size and polar (T) 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 SIFD; loss of CCA tRNA nucleotidyltransferase activity. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 223 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 434 The length of the canonical sequence.
Location on the sequence: help RFYGRIVDKPGDHDPETLEA I AENAKGLAGISGERIWVELK 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                         RFYGRIVDKPGDHDPETLEAIAENAKGLAGISGERIWVELK

Mouse                         RFYGRIVDRPGDHDHETLEAIAENAKGLAGISGERIWVELK

Zebrafish                     RFYGRVAAEPGQHEPETLEAIRENARGLAGISGERIWVELK
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 42 – 434 CCA tRNA nucleotidyltransferase 1, mitochondrial
Binding site 203 – 203
Binding site 203 – 203
Alternative sequence 58 – 434 Missing. In isoform 3.
Helix 217 – 226



Literature citations
Mutations in TRNT1 cause congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD).
Chakraborty P.K.; Schmitz-Abe K.; Kennedy E.K.; Mamady H.; Naas T.; Durie D.; Campagna D.R.; Lau A.; Sendamarai A.K.; Wiseman D.H.; May A.; Jolles S.; Connor P.; Powell C.; Heeney M.M.; Giardina P.J.; Klaassen R.J.; Kannengiesser C.; Thuret I.; Thompson A.A.; Marques L.; Hughes S.; Bonney D.K.; Bottomley S.S.; Wynn R.F.; Laxer R.M.; Minniti C.P.; Moppett J.; Bordon V.; Geraghty M.; Joyce P.B.; Markianos K.; Rudner A.D.; Holcik M.; Fleming M.D.;
Blood 124:2867-2871(2014)
Cited for: INVOLVEMENT IN SIFD; VARIANTS SIFD ILE-154; VAL-158; SER-166; ILE-190; THR-223; THR-326 AND GLU-416; CHARACTERIZATION OF VARIANTS SIFD ILE-154; VAL-158; SER-166; ILE-190; THR-223 AND THR-326; FUNCTION; CATALYTIC ACTIVITY; TRNT1 deficiency: clinical, biochemical and molecular genetic features.
Wedatilake Y.; Niazi R.; Fassone E.; Powell C.A.; Pearce S.; Plagnol V.; Saldanha J.W.; Kleta R.; Chong W.K.; Footitt E.; Mills P.B.; Taanman J.W.; Minczuk M.; Clayton P.T.; Rahman S.;
Orphanet J. Rare Dis. 11:90-90(2016)
Cited for: VARIANTS SIFD ILE-190 AND THR-223; Aberrant tRNA processing causes an autoinflammatory syndrome responsive to TNF inhibitors.
Giannelou A.; Wang H.; Zhou Q.; Park Y.H.; Abu-Asab M.S.; Ylaya K.; Stone D.L.; Sediva A.; Sleiman R.; Sramkova L.; Bhatla D.; Serti E.; Tsai W.L.; Yang D.; Bishop K.; Carrington B.; Pei W.; Deuitch N.; Brooks S.; Edwan J.H.; Joshi S.; Prader S.; Kaiser D.; Owen W.C.; Sonbul A.A.; Zhang Y.; Niemela J.E.; Burgess S.M.; Boehm M.; Rehermann B.; Chae J.; Quezado M.M.; Ombrello A.K.; Buckley R.H.; Grom A.A.; Remmers E.F.; Pachlopnik J.M.; Su H.C.; Gutierrez-Cruz G.; Hewitt S.M.; Sood R.; Risma K.; Calvo K.R.; Rosenzweig S.D.; Gadina M.; Hafner M.; Sun H.W.; Kastner D.L.; Aksentijevich I.;
Ann. Rheum. Dis. 77:612-619(2018)
Cited for: VARIANTS SIFD TRP-99; ILE-110; GLY-128; VAL-163; ARG-215; THR-223 AND GLU-416; In vitro studies of disease-linked variants of human tRNA nucleotidyltransferase reveal decreased thermal stability and altered catalytic activity.
Leibovitch M.; Hanic-Joyce P.J.; Joyce P.B.M.;
Biochim. Biophys. Acta 1866:527-540(2018)
Cited for: VARIANTS SIFD ILE-154; VAL-158; SER-166; ILE-190 AND THR-223; CHARACTERIZATION OF VARIANTS SIFD ILE-154; VAL-158; SER-166; ILE-190 AND THR-223; FUNCTION; CATALYTIC ACTIVITY; BIOPHYSICOCHEMICAL PROPERTIES;
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.