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UniProtKB/Swiss-Prot Q92989: Variant p.Arg140His

Polyribonucleotide 5'-hydroxyl-kinase Clp1
Gene: CLP1
Variant information

Variant position:  140
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  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:  From Arginine (R) to Histidine (H) at position 140 (R140H, p.Arg140His).
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:  Change from large size and basic (R) to medium size and polar (H)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  0
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:  In PCH10; decreases kinase activity, impairs formation of the tRNA splicing endonuclease complex and impairs ability to mediate tRNA splicing and maturation.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  140
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  425
The length of the canonical sequence.

Location on the sequence:   VGPTDVGKSTVCRLLLNYAV  R LGRRPTYVELDVGQGSVSIP
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.

Sequence annotation in neighborhood:  
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 – 425 Polyribonucleotide 5'-hydroxyl-kinase Clp1
Alternative sequence 139 – 202 Missing. In isoform 2.
Mutagenesis 127 – 127 K -> A. Abrogates RNA kinase activity and tRNA splicing activity.
Mutagenesis 151 – 151 D -> A. Abrogates complementation of tRNA splicing activity in yeast.


Literature citations

Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function.
Karaca E.; Weitzer S.; Pehlivan D.; Shiraishi H.; Gogakos T.; Hanada T.; Jhangiani S.N.; Wiszniewski W.; Withers M.; Campbell I.M.; Erdin S.; Isikay S.; Franco L.M.; Gonzaga-Jauregui C.; Gambin T.; Gelowani V.; Hunter J.V.; Yesil G.; Koparir E.; Yilmaz S.; Brown M.; Briskin D.; Hafner M.; Morozov P.; Farazi T.A.; Bernreuther C.; Glatzel M.; Trattnig S.; Friske J.; Kronnerwetter C.; Bainbridge M.N.; Gezdirici A.; Seven M.; Muzny D.M.; Boerwinkle E.; Ozen M.; Clausen T.; Tuschl T.; Yuksel A.; Hess A.; Gibbs R.A.; Martinez J.; Penninger J.M.; Lupski J.R.;
Cell 157:636-650(2014)
Cited for: VARIANT PCH10 HIS-140; FUNCTION; IDENTIFICATION IN THE TRNA SPLICING ENDONUCLEASE COMPLEX; MUTAGENESIS OF LYS-127; CHARACTERIZATION OF VARIANT PCH10 HIS-140;

CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration.
Schaffer A.E.; Eggens V.R.; Caglayan A.O.; Reuter M.S.; Scott E.; Coufal N.G.; Silhavy J.L.; Xue Y.; Kayserili H.; Yasuno K.; Rosti R.O.; Abdellateef M.; Caglar C.; Kasher P.R.; Cazemier J.L.; Weterman M.A.; Cantagrel V.; Cai N.; Zweier C.; Altunoglu U.; Satkin N.B.; Aktar F.; Tuysuz B.; Yalcinkaya C.; Caksen H.; Bilguvar K.; Fu X.D.; Trotta C.R.; Gabriel S.; Reis A.; Gunel M.; Baas F.; Gleeson J.G.;
Cell 157:651-663(2014)
Cited for: VARIANT PCH10 HIS-140; FUNCTION; SUBCELLULAR LOCATION;

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.