UniProtKB/Swiss-Prot Q92989: Variant p.Arg140His

• Variant information
• Sequence information
• Literature citations
• All

Variant information

Variant position: 140 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: LP/P [Disclaimer: Variants classification is intended for research purposes only, not for clinical and diagnostic use. The label disease variant is assigned according to literature reports on probable disease-association that can be based on theoretical reasons. This label must not be considered as a definitive proof for the pathogenic role of a variant.] 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.

• Variant rs587777616 [ dbSNP | Ensembl ]

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.

Type	Positions	Description
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.
Helix	127 – 140

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;